Suppressors of CpG oligonucleotides and methods of use

ABSTRACT

The present disclosure relates to oligodeoxynucleotides that suppress an immune response. Methods are disclosed for preventing or treating an immune-mediated disorder, such as, but not limited to, an autoimmune disease, by administering a therapeutically effective amount of a suppressive oligodeoxynucleotide. Also disclosed are methods of suppressing an immune response in a subject by administering a therapeutically effective amount of a suppressive oligodeoxynucleotide.

PRIORITY CLAIM

This is a continuation of U.S. application Ser. No. 12/395,539, filed onFeb. 27, 2009 now U.S. Pat. No. 8,227,438, which is a divisional of U.S.application Ser. No. 10/489,839, filed on Mar. 16, 2004 now U.S. Pat.No. 7,514,414, which is the §371 U.S. National Stage of InternationalApplication No. P0CT/US02/30532, filed on Sep. 24, 2002, which waspublished in English under PCT Article 21(2), which in turn claims thebenefit of U.S. Provisional Patent Application No. 60/324,484, filed onSep. 24, 2001, and U.S. Provisional Patent Application No. 60/400,826,filed on Aug. 1, 2002. All of the prior applications are incorporated byreference herein in their entirety.

FIELD OF THE DISCLOSURE

The present disclosure relates to oligodeoxynucleotides that suppress animmune response, and to methods of using these oligonucleotides to treatdisorders associated with an immune response.

BACKGROUND

The immune system is composed of many interdependent cell types thatcollectively protect the body from bacterial, parasitic, fungal, viralinfections and from the growth of tumor cells. Many of these cell types,such a B cells, macrophages, an Natural Killer cells, have specializedfunctions. The cells of the immune system can engulf bacteria, killparasites or tumor cells, or kill viral-infected cells. Often, thesecells depend on the T helper subset for activation signals in the formof secretions formally known as cytokines, lymphokines, or morespecifically interleukins.

Cells of the immune system recognize and are activated by conservedpathogen associated molecular patterns (PAMPs) in infectious agents. Theunmethylated CpG dimers embedded in bacterial DNA, as well as certainsynthetic oligodeoxynucleotides (ODNs) containing unmethylated CpGsequences (termed a CpG motif) that emulated them, are more frequent inthe genomes of bacteria and viruses than vertebrates. Recent studiessuggest that immune recognition of these motifs may contribute to thehost's innate immune response (Klinman et al., Proc. Natl. Acad. Sci.USA 93: 2879, 1996; Yi et al., J. Immun. 157: 5394, 1996; Liang et al.,J. Clin. Invest. 98:1119, 1996; Krieg et al., Nature 374: 546, 1995).

In mice, CpG DNA induces proliferation in almost all (>95%) of B cellsand increases immunoglobulin (Ig) secretion. This B-cell activation byCpG DNA is T-cell independent and antigen non-specific. In addition toits direct effects on B cells, CpG DNA has also been shown to activatecells of the immune system (see, for example, International PatentApplications WO 95/26204, WO 96/02555, WO 98/11211, WO 98/18810, WO98/37919, WO 98/40100, WO 98/52581, PCT/US98/047703, and PCT/US99/07335;U.S. Pat. No. 5,663,153).

However, in many situations, there is a need to suppress an immuneresponse. For example, in an autoimmune disease, a foreign antigenmimics one or more self-proteins, and the immune system produces aresponse in which a tissue is consequently injured. Similarly, when asubject is the recipient of a transplanted tissue (e.g. a heart, lung,pancreas, or kidney recipient), the body can produce an immune responseagainst the donor tissue. In this situation, there is a clear need tosuppress the immune response, in order to avoid rejection of the graft.Additionally, there is a need to suppress the immune response in orderto prevent or treat allergic disorders such as asthma.

In view of the above, there exists a need for agents that suppressimmune responses. Specifically, there is a need for agents that can beused to suppress the inflammation, and that can be used to suppress anthe immune response associated with autoimmune diseases, allergies, andtransplant rejection.

BRIEF SUMMARY OF SPECIFIC EMBODIMENTS

Oligodeoxynucleotides are disclosed herein that can be used to suppressimmune activation. These suppressive oligodeoxynucleotides are of use inpreventing and/or treating a variety of diseases and disorders thatinclude, but are not limited to, autoimmune diseases. Specific,non-limiting examples of autoimmune disorders are inflammatoryarthritis, Hashimoto's thyroiditis, pernicious anemia, Addison'sdisease, type I diabetes, systemic lupus erythematosus, dermatomyositis,Sjogren's syndrome, dermatomyositis, lupus erythematosus, multiplesclerosis, myasthenia gravis, Reiter's syndrome, and Grave.s disease,among others. The suppressive oligodeoxynucleotides can be administeredlocally, such as, but not limited to, administration by intra-articularinjection or inhalation, or can be administered systemically.

A substantially pure or isolated oligodeoxynucleotide (ODN) is disclosedherein that is at least about 8 nucleotides in length, forms a G tetrad,has a CD value of greater than 2.9, has at least two guanosines, andsuppresses an immune response. Optionally, the suppressive ODN hasmultiple guanosine-rich sequences, and in some examples, the ODN has oneor more TTAGGG motifs. Furthermore, in particular embodiments, the ODNis modified to prevent degradation or is part of an oligodeoxynucleotidedelivery complex that includes a targeting moiety. In one specific,non-limiting example the suppressive ODN suppresses CpG-DNA-inducedimmune activation.

Also disclosed herein is a pharmacological composition that includes thesuppressive ODN and a pharmacologically acceptable carrier.

In another embodiment, a method is disclosed for treating or preventingan autoimmune disease in a subject. The method includes administering atherapeutically effective amount of the suppressive ODN to a subjecthaving or at risk of developing an autoimmune disease, thereby treatingor preventing the autoimmune disease. In some embodiments, the ODN isadministered orally, intravenously, intra-muscularly, sub-cutaneously,or intra-articularly.

In another embodiment, a method is disclosed for treating or preventingan autoimmune disease in a subject that includes contacting immune cellswith the suppressive ODN in vitro. The immune cells are and transferredto a subject having or at risk of developing an autoimmune disease.

Other embodiments are methods of suppressing an immune response in asubject including administering a therapeutically effective amount of asuppressive ODN to a subject in which it is desirable to suppress animmune response, thereby suppressing the immune response.

Also described herein is a kit for treating or preventing an autoimmunedisease in a subject that includes the suppressive ODN and instructionsfor administering the ODN to a subject.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: is a set of diagrams of the structure of a G-tetrad. FIG. 1A isa diagram of the structure of an individual G-tetrad that shows theHoogsteen base pairing. M⁺ represents a monovalent cation such as K⁺ orNa⁺ and dR is the sugar-phosphate backbone. FIG. 1B is a schematicrepresentation showing the possible folded intramolecular quadruplexstructure. FIG. 1C is a schematic showing the GG-base pair formed bymeans of Hoogsteen hydrogen bonds. FIG. 1D is a schematic of anintramolecular hairpin.

FIG. 2: is a set of graphs showing the factors contributing to thesuppression of CpG-induced immune activation. FIG. 2A is a graph showingthat mammalian DNA suppresses CpG DNA-induced immune activation. FIG. 2Bis a graph showing that the telomeric TTAGGG repetitive motif issuppressive. FIG. 2C is a graph showing that the suppressive motif isactive in trans and cis conformations.

FIG. 2D is a graph showing that suppressive ODNs selectively block CpGDNA-induced immune activation. FIG. 2E is a graph showing that Poly Gsare critical for suppression. FIG. 2F is a graph showing that G-tetradforming non-telomere sequences are also suppressive.

FIG. 3: is a pair of graphs showing that G-tetrad-forming suppressiveODNs selectively suppress CpG-induced immune activation. FIG. 3A is agraph showing that oligonucleotides (ODNs) containing suppressive motifsinhibit CpG-induced immune activation in a dose dependent fashion. FIG.3B is a graph showing G-tetrad formation and suppressive activity ofphosphorothioate and 7-DG modified ODNs.

FIG. 4: is a graph showing the effect of suppressive ODN on CpG DNA andCon A induced IFNγ production. BALB/c spleen cells were stimulated with1 μM CpG ODN (ODN1555, ODN1466), 50 μg/ml of bacterial DNA, or 5 μg/mlCon A. The response of these cultures was compared to cellsco-stimulated with 1 μM of control ODN1612, suppressive ODN1502 orsuppressive ODNH154. The number of IFNγ secreting cells was determinedby ELIspot after 18 h. Data represent the average+SD of triplicatecultures. The experiment was repeated three times with similar results.

FIG. 5: is a graph showing the concentration effects of suppressive ODN.BALB/c spleen cells were stimulated with 1 μM CpG ODN1555 or ODN1466plus increasing amounts of suppressive ODN1502 or ODNH154. Cytokinelevels in culture supernatants were measured by ELISA after 24 h.Results represent the mean+SD of 4 different experiments.

FIG. 6: is a graph showing the kinetics of suppressive ODN. BALB/cspleen cells were stimulated with 1 μM CpG ODN1555. At various times, 1μM suppressive ODN1520 was added. Cytokine levels in culturesupernatants were measured by ELISA after 24 h. Results represent themean of two independent experiments.

FIG. 7: is a graph showing the effect of removing CpG ODN from culturedcells. 1 μM of CpG ODN1555 was added to BALB/c spleen cells at T=0. Thecells were washed free of this ODN after various incubation periods.IFNγ and IL-12 levels in culture supernatants were measured by ELISAafter 24 h. Results represent the average+SD of duplicate cultures.Similar results were obtained in studies of CpG ODN1466.

FIG. 8: is a graph showing that suppressive ODN do not block the bindingor uptake of CpG ODN. BALB/c spleen cells were incubated with 1 μM ofCpG ODN1555 (black bar) plus 1 μM of suppressive ODN1502 (grey bar) orcontrol ODN1612 (white bar). The percent of cells that bound orinternalized the CpG ODN was determined by FACS. Similar results wereobtained using CpG ODN1466, suppressive ODNH154 and control ODN1471.

FIG. 9: is a graph showing that suppressive ODN permit higher levels oftransgene expression.

FIG. 10: is a graph showing that suppressive ODN blocks the activity ofCpG motifs in vivo.

FIG. 11: is a set of graphs showing the effect of CpG ODN andsuppressive ODN injection into the knee. FIG. 11A is a graph of jointswelling in mice treated with CpG ODN (solid circle), CpG plus controlODN (solid square), CpG plus suppressive ODN (open diamond), control ODN(open triangle), suppressive ODN (inverted open triangle), or PBS (opensquare, N=8-11 mice/group). FIG. 11B is a graph showing histologicchanges in the injected knees. Knees were evaluated 4 days aftertreatment by a blinded investigator. Scale: 0; no inflammation, 1;sparse, localized perivascular infiltrate, 2; moderate infiltrate, 3;moderate-dense infiltrate with synovial hyperplasia. FIG. 11C is a graphshowing that suppressive ODNs suppress joint swelling. At T=0, bothknees were injected with 25 g of CpG ODN. The R knee was then injectedwith PBS and the L knee with 25 g of suppressive ODN either 0 (solidcircles, N=3), 24 (solid squares, N=6) or 48 (solid triangles, N=6) hlater. Results show the difference in swelling between the two knees.Statistical significance was assessed by repeated-measures ANOVA usingthe Proc Mixed procedure (A, C) and Wilcoxon Rank sum test (B). *p<0.05.

FIG. 12: is a digital image of a photomicrograph showing the effects ofCpG and ODN injection on knee histology in mice. BALB/c knees wereinjected with PBS (FIG. 12A, B), CpG ODN (FIG. 12C, D), CpG plus controlODN (FIG. 12E, F) or CpG plus suppressive ODN (25 g of each ODN, FIG.12G, H). Typical histology 4 days after injection of 25 μg of each ODNis shown. Note the cellular infiltrates, perivascular accumulation ofmononuclear cells, and hyperplasia of the synovial lining in the kneesof mice injected with CpG ODN. Panels A, C, E and G show 100×magnification; panels B, D, F, H show 400× magnification.

FIG. 13: is a set of graphs that demonstrate that administration ofsuppressive ODN decreases TNFα upregulation following CpG ODN injection.FIG. 13A is a graph of TNFα levels following treatment with ODN. BALB/cspleen cells were stimulated in vitro for 72 h with 1 μM of various ODN.FIG. 13B is a graph of percent TNFα production versus suppressive ODNconcentration. RAW 264.7 cells (106/well) were stimulated with 1 uM CpGplus increasing amounts of suppressive ODN. The concentration of TNF inculture supernatants after 24 h was measured by ELISA. Data representthe mean+SEM of 5 independently studied animals/group. Statisticalsignificance was assessed by Wilcoxon Rank sum test. FIG. 13C is adigital image of an agarose gel. Joints injected with 25 g of ODN wereprocessed into RNA 3 days later. Representative examples of local TNFand β-actin mRNA levels are shown. FIG. 13D is a graph of relative TNFαmRNA expression following treatment with CpG ODN or CpG ODN andsuppressive ODN. Relative intensity of TNFα vs β-actin mRNA (N=3). *p<0.05.

FIG. 14: is a graph showing that the local administration of suppressiveODNs reduces the pro-inflammatory effect of CpG ODN administration.Optimal suppression of CpG ODN-mediated joint inflammation is attainedwhen the suppressive ODN are administered 3 days before the inflammatorychallenge. Shown is the mean and SEM of 10-11 mice/group pre-treatedlocally (intra-articularly) with suppressive ODN 3 days prior to CpG ODNchallenge (open circles), suppressive ODN administered 1 day prior toCpG ODN challenge (open, inverted triangles), suppressive ODNadministered at the time of the CpG ODN challenge (open triangles). Thejoint swelling of mouse knees injected with control ODN (black diamonds)or PBS (black circles) 3 days before the CpG serve as controls.

FIG. 15: is a graph showing that naive mice (and mice pre-treated withcontrol ODN or PBS) developed severe arthritis following local CpG ODNchallenge. In contrast, systemic administration of suppressive ODN threedays prior to local CpG DNA challenge reduced joint swelling andinflammation by 80-85% (p<0.029). BALB/c mice were treated IP with 300μg of suppressive ODN 0-3 days prior to the intra-articular injection of25 μg CpG DNA. Consistent with previous studies, naive mice (and micepre-treated with control ODN or PBS) developed severe arthritisfollowing local CpG ODN challenge.

FIG. 16: is a pair of graphs showing that systemic administration ofsuppressive ODN three days prior to local CpG DNA challenge reducedjoint swelling and inflammation by 80-85% (p<0.029).

FIG. 17: is a pair of graphs showing that systemically administeredsuppressive ODN elicit a population of regulatory cells that inhibitCpG-induced arthritis. As expected, spleen cells from untreated donorshad no effect on the development of CpG-induced arthritis. Bycomparison, the transfer of 20×10⁶ spleen cells from suppressive ODNtreated donors significantly reduced joint swelling and inflammation inthe recipients.

FIG. 18: is a graph showing that CD11c+ cells are responsible for theresistance to CpG-induced arthritis. Magnetic beads were used to depleteor enrich specific cell subpopulations from donor spleens. Depletion ofCD 19+ B cells, T cells, or NK cells had no effect on CpG-inducedarthritis. However, removal of CD11c+ dendritic cells resulted in acomplete abrogation of the suppressive activity of the transferredspleen cell population. Similarly, the transfer of only 5×105 CD11c+enriched cells from suppressive ODN treated mice to normal recipientsconferred resistance to CpG-induced arthritis.

FIG. 19. is a graph showing that neutralizing ODNs inhibit HSVDNA-induced angiogenesis. Pellets containing 1 μg of HSV DNA alone or incombination with 1 μg of control or neutralizing ODN were implanted intocorneal micropockets. The figure shows the average degree ofangiogenesis 4 days after pellet implantation (four to five mice pergroup). *, P<0.01.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING

The Sequence Listing is submitted as an ASCII text file[4239-67747-03_Sequence_Listing.txt, Jun. 21, 2012, 6.74 KB], which isincorporated by reference herein.

SEQ ID NOs 1-25 are suppressive ODN sequences.

SEQ ID NOs 28, 29, and 31 are control ODN sequences.

SEQ ID NOs 26, 27, and 30 are immunostimulatory CpG sequences.

DETAILED DESCRIPTION OF SEVERAL EMBODIMENTS

I. Abbreviations

A: adenine

Ab: antibody

C: cytosine

CD: circular dichroism

CpG ODN: an oligodeoxynucleotide including a CpG motif.

DC: dendritic cell

FCS: fetal calf serum

G: guanine

GI: gastrointestinal

GU: genitourinary

h: hour

IFN-α: interferon alpha

IFN-γ: interferon gamma

IL-10: interleukin 10

mm: millimeter

mRNA: messenger ribonucleic acid.

ODN: oligodeoxynucleotide

Pu: purine

Py: pyrimidine

s.c.: subcutaneous

T: thymine

μg: microgram

II. Terms

Unless otherwise noted, technical terms are used according toconventional usage. Definitions of common terms in molecular biology maybe found in Benjamin Lewin, Genes V, published by Oxford UniversityPress, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.), TheEncyclopedia of Molecular Biology, published by Blackwell Science Ltd.,1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biologyand Biotechnology: a Comprehensive Desk Reference, published by VCHPublishers, Inc., 1995 (ISBN 1-56081-569-8).

Unless otherwise explained, all technical and scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which this disclosure belongs. The singular terms“a,” “an,” and “the” include plural referents unless context clearlyindicates otherwise. Similarly, the word “or” is intended to include“and” unless the context clearly indicates otherwise. It is further tobe understood that all base sizes or amino acid sizes, and all molecularweight or molecular mass values, given for nucleic acids or polypeptidesare approximate, and are provided for description. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present disclosure, suitable methods andmaterials are described below. In case of conflict, the presentspecification, including explanations of terms, will control. Inaddition, the materials, methods, and examples are illustrative only andnot intended to be limiting.

In order to facilitate review of the various embodiments of thedisclosure, the following explanations of specific terms are provided:

Allergy: An example of an immune-mediated disorder. An allergy is acollection of symptoms caused by an exaggerated immune response orreaction to substances that do not trigger an immune response in mostpeople. The term “allergy” has become synonymous with Type Ihypersensitivity (IgE-mediated allergy). Four different types ofhypersensitivity were described by Coomb and Gell (Types I, II, III andIV), as a pedagogical way to increase the understanding of differentimmune reactions which could be provoked by many antigens. In practicethese types do not necessarily occur in isolation from each other.

Allergic diseases generally begin in childhood, although they can ariseat any age. Development of allergic disease is associated with anallergic constitution due to heredity and to environmental and healthfactors. An allergic response involves an increased production ofallergen-specific IgE antibodies, which may lead to clinical symptomssuch as rhinitis, asthma, eczema, colic pains or diarrhea. A state ofhyperreactivity often accompanies an allergic reaction. If thishyperreactivity occurs in the respiratory tract, everyday stimuli likedust, tobacco smoke, cold air and perfumes may lead to allergy-likesymptoms.

Animal: Living multi-cellular vertebrate organisms, a category thatincludes, for example, mammals and birds. The term mammal includes bothhuman and non-human mammals. Similarly, the term “subject” includes bothhuman and veterinary subjects.

Angiogenesis: A process leading to the generation of new blood vesselsthrough sprouting from already existing blood vessels. The processinvolves the migration and proliferation of endothelial cells frompreexisting vessels. Angiogenesis occurs both during pre-nataldevelopment, post-natal development, and in the adult. In the adultangiogenesis occurs during the normal cycle of the female reproductivesystem, wound healing, and during pathological processes such as cancer(for review see Battegay, J. Molec. Med. 73(7): 333-346, 1995; Beck andD'Amore, FASEB J. 11(5): 365, 1997)

Angiogenic Factor: A molecule that promotes angiogenesis. A plethora ofexperiments have suggested that tissues secrete factors which promoteangiogenesis under conditions of poor blood supply during normal andpathological angiogenesis processes. Angiogenic molecules are generatedby tumor, inflammatory, and connective tissue cells in response tohypoxia and other as-yet ill-defined stimuli. The first indication ofthe existence of such diffusible substances was gleaned from filtrationexperiments demonstrating that tumor cells separated from underlyingtissues by filters that do not allow passage of cells are neverthelesscapable of supporting vessel growth in these tissues. The formation ofblood vessels is initiated and maintained by a variety of factorssecreted either by the tumor cells themselves or by accessory cells.Many different growth factors and cytokines have been shown to exertchemotactic, mitogenic, modulatory or inhibitory activities onendothelial cells, smooth muscle cell and fibroblasts and can,therefore, be expected to participate in an angiogenic process in oneway or another. For example, factors modulating growth, chemotacticbehavior and/or functional activities of vascular endothelial cellsinclude αFGF, βFGF, angigiogenein, angiotropin, epithelial growthfactor, IL-8, and vascular endothelial growth factor (VEGF), amongstothers.

As many angiogenic factors are mitogenic and chemotactic for endothelialcells their biological activities can be determined in vitro bymeasuring the induced migration of endothelial cells or the effect ofthese factor on endothelial cell proliferation. Alternatively, abioassay may be utilized for direct determination of angiogenicactivities and permit repeated, long-term quantitation of angiogenesisas well as physiological characterization of angiogenic vessels. Manysuch assays are known in the art.

One assay employs the use of a non-vascularized mouse eye (e.g. Kenyonet al., Invest Opthalmol. Vis. Sci. 37:1625, 1996; also see Examplessection) or the rabbit eye (e.g., see Gaudric et al., Ophthal. Res. 24:181, 1992), and is termed a cornea pocket assay. This assay has theadvantage that new blood vessels are easily detected and essentiallymust be newly formed blood vessels in the normally avascular cornea.Another assay involves the use of chicken chorioallantoic membrane (theCAM assay; see Wilting et al., Anat. Embryol. 183: 259, 1991). Otherassays in the rat, such as the rat aortic ring model, providereproducible assays that are often utilized to identify angiogenicagonists and antagonists (e.g. see Lichtenberg et al., PharmacolToxicol. 84: 34, 1999).

Antigen: A compound, composition, or substance that can stimulate theproduction of antibodies or a T-cell response in an animal, includingcompositions that are injected or absorbed into an animal. An antigenreacts with the products of specific humoral or cellular immunity,including those induced by heterologous immunogens. The term “antigen”includes all related antigenic epitopes.

Antisense, Sense, and Antigene: Double-stranded DNA (dsDNA) has twostrands, a 5′->3′ strand, referred to as the plus strand, and a 3′->5′strand (the reverse compliment), referred to as the minus strand.Because RNA polymerase adds nucleic acids in a 5′->3′ direction, theminus strand of the DNA serves as the template for the RNA duringtranscription. Thus, the RNA formed will have a sequence complementaryto the minus strand and identical to the plus strand (except that U issubstituted for T).

Antisense molecules are molecules that are specifically hybridizable orspecifically complementary to either RNA or the plus strand of DNA.Sense molecules are molecules that are specifically hybridizable orspecifically complementary to the minus strand of DNA. Antigenemolecules are either antisense or sense molecules directed to a dsDNAtarget. In one embodiment, an antisense molecule specifically hybridizesto a target mRNA and inhibits transcription of the target mRNA.

Arthritis: Arthritis is an inflammatory disease that affects thesynovial membranes of one or more joints in the body. It is the mostcommon type of joint disease, and it is characterized by theinflammation of the joint. The disease is usually oligoarticular(affects few joints), but may be generalized. The joints commonlyinvolved include the hips, knees, lower lumbar and cervical vertebrae,proximal and distal interphangeal joints of the fingers, firstcarpometacarpal joints, and first tarsometatarsal joints of the feet.

One type of arthritis is reactive arthritis, which is an acutenonpurulent arthritis secondary to a urinary tract or gastrointestinalinfection with a variety of microorganisms, including Chlamydiatrachomatis, Yersinia, Salmonella, Shigella, and Campylobacter.Microbial components are found in the affected joints. The arthritisappears abruptly and tends to involve the knees and ankles, butsometimes involves the wrists, fingers, and/or toes. Untreated, thearthritis lasts for about a year, then generally abates and only rarelyis accompanied by ankylosing spondylitis. Despite evidence of diseasebeing triggered by bacterial infection, viable bacteria are rarelypresent in affected joints and antibiotic treatment seldom providesrelief.

Another type of arthritis is rheumatoid arthritis. Rheumatoid arthritisis a chronic, systemic, inflammatory disease that affects the synovialmembranes of multiple joints in the body. Because the disease issystemic, there are many extra-articular features of the disease aswell. For example, neuropathy, scleritis, lymphadenopathy, pericarditis,splenomegaly, arteritis, and rheumatoid nodules are frequent componentsof the disease. In most cases of rheumatoid arthritis, the subject hasremissions and exacerbations of the symptoms. Rheumatoid arthritisconsidered an autoimmune disease that is acquired and in which geneticfactors appear to play a role.

Autoimmune disorder: A disorder in which the immune system produces animmune response (e.g., a B cell or a T cell response) against anendogenous antigen, with consequent injury to tissues. For example,rheumatoid arthritis is an autoimmune disorder, as are Hashimoto'sthyroiditis, pernicious anemia, Addison's disease, type I diabetes,systemic lupus erythematosus, dermatomyositis, Sjogren's syndrome,dermatomyositis, lupus erythematosus, multiple sclerosis, myastheniagravis, Reiter's syndrome, and Grave.s disease, among others.

CD value: The formation of G-tetrads yields a complex with differentphysical properties than the individual oligonucleotides.Spectroscopically, this is manifested by an increase in circulardicroism (CD), and an increase in peak absorbance to the 260-280 nmwavelength owing to the formation of secondary structures. Thus, aconvenient method for identifying oligonucleotides that form G-tetradsis to study their CD values. An increase in peak ellipticity values togreater than 2.0 is typical of a G-tetrad forming oligonucleotide. Thehigher the ellipticity value, the greater the tetrad-forming capacity ofthe oligonucleotide.

CpG or CpG motif: A nucleic acid having a cytosine followed by a guaninelinked by a phosphate bond in which the pyrimidine ring of the cytosineis unmethylated. The term “methylated CpG” refers to the methylation ofthe cytosine on the pyrimidine ring, usually occurring the 5-position ofthe pyrimidine ring. A CpG motif is a pattern of bases that include anunmethylated central CpG surrounded by at least one base flanking (onthe 3′ and the 5′ side of) the central CpG. Without being bound bytheory, the bases flanking the CpG confer part of the activity to theCpG oligodeoxynucleotide. A CpG oligonucleotide is an oligonucleotidethat is at least about ten nucleotides in length and includes anunmethylated CpG. CpG oligonucleotides include both D and K typeoligodeoxynucleotides (see below). CpG oligodeoxynucleotides aresingle-stranded. The entire CpG oligodeoxynucleotide can be unmethylatedor portions may be unmethylated. In one embodiment, at least the C ofthe 5′ CG 3′ is unmethylated.

Cytokine: Proteins made by cells that affect the behavior of othercells, such as lymphocytes. In one embodiment, a cytokine is achemokine, a molecule that affects cellular trafficking.

Epitope: An antigenic determinant. These are particular chemical groupsor peptide sequences on a molecule that are antigenic, i.e., that elicita specific immune response. An antibody binds a particular antigenicepitope.

Functionally Equivalent Sequence alterations, for example in asuppressive ODN, that yield the same results as described herein. Suchsequence alterations can include, but are not limited to, deletions,base modifications, mutations, labeling, and insertions.

Graft-versus-host disease: Tissue rejection, also calledgraft-versus-host disease, is a consequence of organ or tissuetransplantation caused by the transplant recipient's (host's) immuneresponse to the transplanted organ/tissue which can damage or destroyit. Ordinarily, the immune response protects the body from potentiallyharmful substances (antigens) such as microorganisms, toxins, and cancercells. The immune system distinguishes “self” from “foreign” by reactingto proteins on the surfaces of cells. It reacts against substances itrecognizes as foreign (antigens). The presence of foreign blood ortissue in the body triggers an immune response that can result in bloodtransfusion reactions and transplant rejection when antibodies areformed against foreign antigens on the transplanted or transfusedmaterial.

G-tetrad: G-tetrads are G-rich DNA segments that can accommodate complexsecondary and/or tertiary structures (see FIG. 1). A G-tetrad involvesthe planar association of four Gs in a cyclic Hoogsteen hydrogen bondingarrangement (this involves non-Watson Crick base-pairing). In general,either a run of two or more contiguous Gs or a hexameric region inwhich >50% of the bases are Gs, is needed for an ODN to form a G-tetrad.The longer the run of contiguous Gs, and the higher the G content of theODN, the higher the likelihood of G-tetrad formation, as reflected byhigher CD or ellipticity values.

Oligonucleotides that form G-tetrads can also form higher-levelaggregates that are more easily recognized and taken up by immune cells,for example, through scavenger receptors or by nucleolin.

Guanosine-rich sequence: A hexameric region of a nucleotide sequence inwhich >50% of the bases are Gs.

Immunostimulatory CpG ODN: An oligodeoxynucleotide, which contains acytosine, guanine dinucleotide sequence and stimulates (e.g., has amitogenic effect) vertebrate immune cells. The cytosine, guanine isunmethylated. Both D and K type CpG ODNs are immunostimulatory (see inVerthelyi et al., J. Immunol. 166:2372-2377, 2001, which is hereinincorporated by reference).

Immunosuppressive agent: A molecule, such as a chemical compound, smallmolecule, steroid, nucleic acid molecule, or other biological agent,that can decrease an immune response such as an inflammatory reaction.

Immunosuppressive agents include, but are not limited to an agent of usein treating arthritis (anti-arthritis agent). Specific, non-limitingexamples of immunosuppressive agents are non-steroidal anti-inflammatoryagents, cyclosporine A, FK506, and anti-CD4. In additional examples, theagent is a biological response modifier, such as Kineret® (anakinra),Enbrel® (etanercept), or Remicade® (infliximab), a disease-modifyingantirheumatic drug (DMARD), such as Arava® (leflunomide), a nonsteroidalanti-inflammatory drug (NSAIDs), specifically a Cyclo-Oxygenase-2(COX-2) inhibitor, such as Celebrex® (celecoxib) and Vioxx® (rofecoxib),or another product, such as Hyalgan® (hyaluronan) and Synvisc® (hylanG-F20).

Immune-Mediated disorder: A disorder that involves an unwanted immuneresponse. Although immune recognition of “non-self” proteins isessential to avoid and eliminate infection, the immune response cansometimes be unwanted. Autoimmune diseases, such as rheumatoidarthritis, multiple sclerosis or insulin dependent diabetes mellitus,are the result of a pathological immune response against self antigens,and T cells are the primary mediators of autoimmunity. For example,rheumatoid arthritis is an autoimmune disorder, as are Hashimoto'sthyroiditis, pernicious anemia, Addison's disease, type I diabetes,systemic lupus erythematosus, dermatomyositis, Sjogren's syndrome,dermatomyositis, lupus erythematosus, multiple sclerosis, myastheniagravis, Reiter's syndrome, and Grave.s disease, among others.

Rejection of transplanted organs and tissues are a further example of animmune-mediated disorder, and can often result in damage to and/orrejection of the transplant. Tissue rejection, also calledgraft-versus-host disease, is a consequence of organ or tissuetransplantation caused by the transplant recipient's (host's) immuneresponse to the transplanted organ/tissue which can damage or destroyit. Ordinarily, the immune response protects the body from potentiallyharmful substances (antigens) such as microorganisms, toxins, and cancercells. The immune system distinguishes “self” from “foreign” by reactingto proteins on the surfaces of cells. It reacts against substances itrecognizes as foreign (antigens). The presence of foreign blood ortissue in the body triggers an immune response that can result in bloodtransfusion reactions and transplant rejection when antibodies areformed against foreign antigens on the transplanted or transfusedmaterial. Before transplant, tissue is “typed” according to the antigensit contains (Histocompatibility antigens).

No two people (except identical twins) have identical tissue antigens.Therefore, in the absence of immunosuppressive drugs, organ and tissuetransplantation would almost always causes an immune response againstthe foreign tissue (rejection), which would result in destruction of thetransplant. Though tissue typing ensures that the organ or tissue is assimilar as possible to the tissues of the recipient, unless the donor isan identical twin, no match is perfect and the possibility oforgan/tissue rejection remains. Immunosuppressive therapy is used toprevent organ rejection.

Allergy is another example of an immune-mediated disorder. An allergy isa collection of symptoms caused by an exaggerated immune response orreaction to substances that do not trigger an immune response in mostpeople. The term “allergy” has become synonymous with Type Ihypersensitivity (IgE-mediated allergy). Four different types ofhypersensitivity were described by Coomb and Gell (Types I, II, III andIV), as a pedagogical way to increase the understanding of differentimmune reactions which could be provoked by many antigens. In practicethese types do not necessarily occur in isolation from each other.

Allergic diseases generally begin in childhood, although they can ariseat any age. Development of allergic disease is associated with anallergic constitution due to heredity and to environmental and healthfactors. An allergic response involves an increased production ofallergen-specific IgE antibodies, which may lead to clinical symptomssuch as rhinitis, asthma, eczema, colic pains or diarrhea. A state ofhyperreactivity often accompanies an allergic reaction. If thishyperreactivity occurs in the respiratory tract, everyday stimuli likedust, tobacco smoke, cold air and perfumes may lead to allergy-likesymptoms.

Immune response: A response of a cell of the immune system, such as a Bcell, T cell to a stimulus. In one embodiment, the response is specificfor a particular antigen (an “antigen-specific response”).

Inflammation: When damage to tissue occurs, the body's response to thedamage is usually inflammation. The damage may be due to trauma, lack ofblood supply, hemorrhage, autoimmune attack, transplanted exogenoustissue or infection. This generalized response by the body includes therelease of many components of the immune system (e.g., IL-1 and TNF),attraction of cells to the site of the damage, swelling of tissue due tothe release of fluid and other processes.

Inflammatory arthropathy: An inflammatory arthropathy is an inflammatorydisease affecting one or more joints, for example an inflammatorydisease that affects the synovial membranes of one or more joints.Inflammatory arthropathies include, for example, arthritis, ankylosingspondylitis, Reiter's syndrome, psoriatic arthropathy, enteropathisspondylitis, juvenile arthropathy, and reactive arthropathy.

Infectious agent: An agent that can infect a subject, including, but notlimited to, viruses, bacteria, and fungi.

Examples of infectious virus include: Retroviridae (for example, humanimmunodeficiency viruses, such as HIV-1 (also referred to as HTLV-III,LAV or HTLV-III/LAV, or HIV-III; and other isolates, such as HIV-LP;Picornaviridae (for example, polio viruses, hepatitis A virus;enteroviruses, human coxsackie viruses, rhinoviruses, echoviruses);Calciviridae (such as strains that cause gastroenteritis); Togaviridae(for example, equine encephalitis viruses, rubella viruses); Flaviridae(for example, dengue viruses, encephalitis viruses, yellow feverviruses); Coronaviridae (for example, coronaviruses); Rhabdoviridae (forexample, vesicular stomatitis viruses, rabies viruses); Filoviridae (forexample, ebola viruses); Paramyxoviridae (for example, parainfluenzaviruses, mumps virus, measles virus, respiratory syncytial virus);Orthomyxoviridae (for example, influenza viruses); Bungaviridae (forexample, Hantaan viruses, bunga viruses, phleboviruses and Nairoviruses); Arena viridae (hemorrhagic fever viruses); Reoviridae (e.g.,reoviruses, orbiviurses and rotaviruses); Birnaviridae; Hepadnaviridae(Hepatitis B virus); Parvoviridae (parvoviruses); Papovaviridae(papilloma viruses, polyoma viruses); Adenoviridae (most adenoviruses);Herpesviridae (herpes simplex virus (HSV) 1 and HSV-2, varicella zostervirus, cytomegalovirus (CMV), herpes viruses); Poxyiridae (variolaviruses, vaccinia viruses, pox viruses); and Iridoviridae (such asAfrican swine fever virus); and unclassified viruses (for example, theetiological agents of Spongiform encephalopathies, the agent of deltahepatitis (thought to be a defective satellite of hepatitis B virus),the agents of non-A, non-B hepatitis (class 1=internally transmitted;class 2=parenterally transmitted (i.e., Hepatitis C); Norwalk andrelated viruses, and astroviruses).

Examples of infectious bacteria include: Helicobacter pyloris, Boreliaburgdorferi, Legionella pneumophilia, Mycobacteria sps (such as. M.tuberculosis, M. avium, M. intracellulare, M. kansaii, M. gordonae),Staphylococcus aureus, Neisseria gonorrhoeae, Neisseria meningitidis,Listeria monocytogenes, Streptococcus pyogenes (Group A Streptococcus),Streptococcus agalactiae (Group B Streptococcus), Streptococcus(viridans group), Streptococcus faecalis, Streptococcus bovis,Streptococcus (anaerobic sps.), Streptococcus pneumoniae, pathogenicCampylobacter sp., Enterococcus sp., Haemophilus influenzae, Bacillusantracis, corynebacterium diphtheriae, corynebacterium sp.,Erysipelothrix rhusiopathiae, Clostridium perfringers, Clostridiumtetani, Enterobacter aerogenes, Klebsiella pneumoniae, Pasturellamultocida, Bacteroides sp., Fusobacterium nucleatum, Streptobacillusmoniliformis, Treponema pallidium, Treponema pertenue, Leptospira, andActinomyces israelli.

Examples of infectious fungi include, but are not limited to,Cryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis,Blastomyces dermatitidis, Chlamydia trachomatis, Candida albicans.

Other infectious organisms (such as protists) include: Plasmodiumfalciparum and Toxoplasma gondii.

Isolated: An “isolated” biological component (such as a nucleic acid,peptide or protein) has been substantially separated, produced apartfrom, or purified away from other biological components in the cell ofthe organism in which the component naturally occurs, i.e., otherchromosomal and extrachromosomal DNA and RNA, and proteins. Nucleicacids, peptides and proteins which have been “isolated” thus includenucleic acids and proteins purified by standard purification methods.The term also embraces nucleic acids, peptides and proteins prepared byrecombinant expression in a host cell as well as chemically synthesizednucleic acids.

Leukocyte: Cells in the blood, also termed “white cells,” that areinvolved in defending the body against infective organisms and foreignsubstances. Leukocytes are produced in the bone marrow. There are 5 maintypes of white blood cell, subdivided between 2 main groups:polymorphonuclear leukocytes (neutrophils, eosinophils, basophils) andmononuclear leukocytes (monocytes and lymphocytes). When an infection ispresent, the production of leukocytes increases.

Mammal: This term includes both human and non-human mammals. Similarly,the term “subject” includes both human and veterinary subjects.

Maturation: The process in which an immature cell, such as dendriticcell, changes in form or function to become a functional mature cell,such as an APC.

Nucleic acid: A deoxyribonucleotide or ribonucleotide polymer in eithersingle or double stranded form, and unless otherwise limited,encompasses known analogues of natural nucleotides that hybridize tonucleic acids in a manner similar to naturally occurring nucleotides.

Oligonucleotide or “oligo”: Multiple nucleotides (i.e., moleculescomprising a sugar (e.g., ribose or deoxyribose) linked to a phosphategroup and to an exchangeable organic base, which is either a substitutedpyrimidine (Py) (e.g., cytosine (C), thymine (T) or uracil (U)) or asubstituted purine (Pu) (e.g., adenine (A) or guanine (G)). The term“oligonucleotide” as used herein refers to both oligoribonucleotides(ORNs) and oligodeoxyribonucleotides (ODNs). The term “oligonucleotide”also includes oligonucleosides (i.e., an oligonucleotide minus thephosphate) and any other organic base polymer. Oligonucleotides can beobtained from existing nucleic acid sources (e.g., genomic or cDNA), butare preferably synthetic (e.g., produced by oligonucleotide synthesis).

A “stabilized oligonucleotide” is an oligonucleotide that is relativelyresistant to in vivo degradation (for example via an exo- orendo-nuclease). In one embodiment, a stabilized oligonucleotide has amodified phosphate backbone. One specific, non-limiting example of astabilized oligonucleotide has a phosphorothioate modified phosphatebackbone (wherein at least one of the phosphate oxygens is replaced bysulfur). Other stabilized oligonucleotides include: nonionic DNAanalogs, such as alkyl- and aryl-phosphonates (in which the chargedphosphonate oxygen is replaced by an alkyl or aryl group), phophodiesterand alkylphosphotriesters, in which the charged oxygen moiety isalkylated. Oligonucleotides which contain a diol, such astetraethyleneglycol or hexaethyleneglycol, at either or both terminihave also been shown to be substantially resistant to nucleasedegradation.

An “immunostimulatory oligonucleotide,” “immunostimulatory CpGcontaining oligodeoxynucleotide,” “CpG ODN,” refers to anoligodeoxynucleotide, which contains a cytosine, guanine dinucleotidesequence and stimulates (e.g., has a mitogenic effect) vertebrate immunecells. The cytosine, guanine is unmethylated.

An “oligonucleotide delivery complex” is an oligonucleotide associatedwith (e.g., ionically or covalently bound to; or encapsulated within) atargeting means (e.g., a molecule that results in a higher affinitybinding to a target cell (e.g., B-cell or natural killer (NK) cell)surface and/or increased cellular uptake by target cells). Examples ofoligonucleotide delivery complexes include oligonucleotides associatedwith: a sterol (e.g., cholesterol), a lipid (e.g., cationic lipid,virosome or liposome), or a target cell specific binding agent (e.g., aligand recognized by a target cell specific receptor). Preferredcomplexes must be sufficiently stable in vivo to prevent significantuncoupling prior to internalization by the target cell. However, thecomplex should be cleavable or otherwise accessible under appropriateconditions within the cell so that the oligonucleotide is functional.(Gursel, J. Immunol. 167: 3324, 2001)

Parenteral: Administered outside of the intestine, e.g., not via thealimentary tract. Generally, parenteral formulations are those that willbe administered through any possible mode except ingestion. This termespecially refers to injections, whether administered intravenously,intrathecally, intramuscularly, intraperitoneally, intra-articularly, orsubcutaneously, and various surface applications including intranasal,intradermal, and topical application, for instance.

Pharmaceutical agent or drug: A chemical compound or composition capableof inducing a desired therapeutic or prophylactic effect when properlyadministered to a subject. Pharmaceutical agents include, but are notlimited to, chemotherapeutic agents and anti-infective agents.

Pharmaceutically acceptable carriers: The pharmaceutically acceptablecarriers useful in this disclosure are conventional. Remington'sPharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton,Pa., 15th Edition (1975), describes compositions and formulationssuitable for pharmaceutical delivery of the fusion proteins hereindisclosed.

In general, the nature of the carrier will depend on the particular modeof administration being employed. For instance, parenteral formulationsusually comprise injectable fluids that include pharmaceutically andphysiologically acceptable fluids such as water, physiological saline,balanced salt solutions, aqueous dextrose, glycerol or the like as avehicle. For solid compositions (e.g., powder, pill, tablet, or capsuleforms), conventional non-toxic solid carriers can include, for example,pharmaceutical grades of mannitol, lactose, starch, or magnesiumstearate. In addition to biologically-neutral carriers, pharmaceuticalcompositions to be administered can contain minor amounts of non-toxicauxiliary substances, such as wetting or emulsifying agents,preservatives, and pH buffering agents and the like, for example sodiumacetate or sorbitan monolaurate.

Preventing or treating a disease: “Preventing” a disease refers toinhibiting the full development of a disease, for example in a personwho is known to have a predisposition to a disease such as an autoimmunedisorder. An example of a person with a known predisposition is someonewith a history of diabetes in the family, or who has been exposed tofactors that predispose the subject to a condition, such as lupus orarthritis. “Treatment” refers to a therapeutic intervention thatameliorates a sign or symptom of a disease or pathological conditionafter it has begun to develop.

Purified: The term purified does not require absolute purity; rather, itis intended as a relative term. Thus, for example, a purified peptidepreparation is one in which the peptide or protein is more enriched thanthe peptide or protein is in its natural environment within a cell.Preferably, a preparation is purified such that the protein or peptiderepresents at least 50% of the total peptide or protein content of thepreparation.

Suppressive ODN: DNA molecules of at least eight nucleotides in length,wherein the oligodeoxynucleotide forms a G-tetrad, and has a CD value ofgreater than about 2.9. In a suppressive ODN the number of guanosines isat least two. In one embodiment, a suppressive ODN inhibits immuneactivation caused by CpG DNA when administered prior to, concurrentlywith, or after the administration of an CpG ODN. at least about 8nucleotides in length.

Therapeutic agent: Used in a generic sense, it includes treating agents,prophylactic agents, and replacement agents.

Therapeutically effective amount of [a compound]: A quantity of aspecified compound sufficient to achieve a desired effect in a subjectbeing treated. For instance, this can be the amount of a suppressive ODNnecessary to suppress CpG-induced immune cell activation in a subject,or a dose sufficient to prevent advancement, or to cause regression of adisease, or which is capable of relieving symptoms caused by a disease,such as pain or swelling.

An effective amount of a suppressive ODN can be administeredsystemically or locally. In addition, an effective amount of asuppressive ODN can be administered in a single dose, or in severaldoses, for example daily, during a course of treatment. However, theeffective amount of the ODN will be dependent on the preparationapplied, the subject being treated, the severity and type of theaffliction, and the manner of administration of the compound. Forexample, a therapeutically effective amount of a suppressive ODN canvary from about 0.01 mg/kg body weight to about 1 g/kg body weight insome embodiments, or from about 0.01 mg/kg to about 60 mg/kg of bodyweight, based on efficacy.

The suppressive ODNs disclosed herein have equal applications in medicaland veterinary settings. Therefore, the general terms “subject” and“subject being treated” are understood to include all animals, includinghumans or other simians, dogs, cats, horses, and cows.

Therapeutically effective dose: A dose sufficient to preventadvancement, or to cause regression of the disease, or which is capableof relieving symptoms caused by the disease, such as pain or swelling.

III. Description of Several Embodiments

A. Suppressive Oligodeoxynucleotides and Guanosine-quadruplexes(G-tetrads)

The present disclosure relates to a class of DNA motifs that selectivelyinhibits or suppresses immune activation. Optimal activity is observedusing multimers of these motifs, which are rich in G bases and capableof forming G-quadruplexes (G-tetrads). G-tetrads are G-rich DNA segmentsthat can accommodate complex secondary and/or tertiary structures (seeFIG. 1). The suppressive ODNs of the disclosure are highly specific(i.e., are neither toxic nor non-specifically immunosuppressive), andare useful for inhibiting an immune response. In one embodiment, asuppressive ODN is of use for blocking immunostimulation caused by CpGmotifs in vivo and in vitro.

A G-tetrad involves the planar association of four Gs in a cyclicHoogsteen hydrogen bonding arrangement (this involves non-Watson Crickbase-pairing). In general, either a run of two or more contiguous Gs ora hexameric region in which>50% of the bases are Gs, is needed for anODN to form a G-tetrad. The longer the run of continuous Gs, and thehigher the G content of the ODN, the higher the likelihood of G-tetradformation, as reflected by higher ellipticity values. Oligonucleotidesthat form G-tetrads can also form higher-level aggregates that are moreeasily recognized and taken up by immune cells, for example, throughscavenger receptors or by nucleolin.

The formation of G-tetrads yields a complex with different physicalproperties than the individual oligonucleotides. Spectroscopically, thisis manifested by an increase in circular dicroism (CD), and an increasein peak absorbance to the 260-280 nm wavelength owing to the formationof secondary structures. Thus, a convenient method for identifyingoligonucleotides that form G-tetrads is to study their CD values. Anincrease in peak ellipticity values to greater than 2.0 is typical of aG-tetrad forming oligonucleotide. For instance, G-tetrad-forming ODNscan have CD values of 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.5, 4.0, 4.5, 5.0,5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, or higher. The higher theellipticity value, the greater the tetrad-forming capacity of theoligonucleotide, so an ODN with a CD value of 8.5 is typically moresuppressive than an ODN with a CD value of 2.9.

In some embodiments, the ODN is from about 8 to about 120 nucleotides inlength. In particular examples, the ODN is from about 10 to about 30nucleotides in length. Optionally, the suppressive ODN has multipleguanosine-rich sequences, for example, in certain embodiments the ODNhas from about two to about 20 guanosine-rich sequences, or, moreparticularly, from about two to about four guanosine-rich sequences.

In one embodiment, the suppressive ODNs have a sequence comprising atleast one of the human telomere-derived TTAGGG suppressive motifs (seeExample 1). In some examples, the ODN has at least one TTAGGG motif, andin certain examples, the ODN has multiple TTAGGG motifs. For example, inparticular examples, the ODN has from about two to about 20 TTAGGGmotifs, or from about two to about four TTAGGG motifs. In thisembodiment, suppressive ODNs containing multiple TTAGGG repeats are themost suppressive. Single TTAGGG motifs are suppressive only whenincorporated into larger ODNs with greater than 10 bases. The TTAGGGmotifs may be in either the cis or trans position, i.e., they may bepresent on the same or on a different strand of DNA than that expressingthe stimulatory CpG sequence.

Suppression of CpG-induced immune activation requires a G-tetrad-formingsequence that imposes the two-dimensional structure necessary forG-tetrad formation. Examples of suppressive ODN include, but are notlimited to, those shown in FIG. 9. However, any oligonucleotide capableof forming G-tetrads may be used to suppress CpG DNA-induced immuneactivation. In particular examples, the ODN has a sequence selected fromthe group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ IDNO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ IDNO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18,SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO:23, SEQ ID NO: 24, and SEQ ID NO: 25.

Furthermore, in particular embodiments the ODN is modified to preventdegradation. In one embodiment, suppressive ODNs can include modifiednucleotides to confer resistance to degradation. Without being bound bytheory, modified nucleotides can be included to increase the stabilityof a suppressive ODN. Thus, because phosphorothioate-modifiednucleotides confer resistance to exonuclease digestion, the suppressiveODNs are “stabilized” by incorporating phosphorothioate-modifiednucleotides.

In some embodiments, the ODN has a phosphate backbone modification, andin particular examples, the phosphate backbone modification is aphosphorothioate backbone modification. In one embodiment, theguanosine-rich sequence and its immediate flanking regions includephosphodiester rather than phosphorothioate nucleotides. In one specificnon-limiting example, the sequence TTAGGG includes phosphodiester bases.In some examples, all of the bases in an ODN are phosphodiester bases.In other examples, the ODN is a phosphorothioate/phosphodiester chimera.

As disclosed herein, any suitable modification can be used to render theODN resistant to degradation in vivo (e.g., via an exo- orendo-nuclease). In one specific, non-limiting example, a modificationthat renders the ODN less susceptible to degradation is the inclusion ofnontraditional bases such as inosine and quesine, as well as acetyl-,thio- and similarly modified forms of adenine, cytidine, guanine,thymine, and uridine. Other modified nucleotides include nonionic DNAanalogs, such as alkyl or aryl phosphonates (i.e., the chargedphosphonate oxygen is replaced with an alkyl or aryl group, as set forthin U.S. Pat. No. 4,469,863), phosphodiesters and alkylphosphotriesters(i.e., the charged oxygen moiety is alkylated, as set forth in U.S. Pat.No. 5,023,243 and European Patent No. 0 092 574). ODNs containing adiol, such as tetraethyleneglycol or hexaethyleneglycol, at either orboth termini, have also been shown to be more resistant to degradation.

The suppressive ODN of the disclosure can be synthesized by standardmethods well known in the art. Most commonly, synthesis is performed onan oligonucleotide synthesizer using the standard cyanoethylphosphoramidite chemistry. These include, but are not limited to,phosphodiester, phosphorothioate, peptide nucleic acids, syntheticpeptide analogues, and any combination thereof. Those skilled in the artwill recognize that any other standard technique may be used tosynthesize the suppressive ODN described herein.

In one embodiment, a suppressive ODN is included in a delivery complex.The delivery complex can include the suppressive ODN and a targetingmeans. Any suitable targeting means can be used. For example, in someembodiments, a suppressive ODN is associated with (e.g., ionically orcovalently bound to, or encapsulated within) a targeting means (e.g., amolecule that results in higher affinity binding to a target cell, suchas a B cell). A variety of coupling or cross-linking agents can be usedto form the delivery complex, such as protein A, carbodiamide, andN-succinimidyl-3-(2-pyridyldithio) propionate (SPDP). Examples ofoligodeoxynucleotide delivery complexes include a suppressive ODNassociated with a sterol (e.g., cholesterol), a lipid (e.g., a cationiclipid, anionic lipid, virosome or liposome), and a target cell specificbinding agent (e.g., a ligand recognized by target cell specificreceptor). Without being bound by theory, the complex is sufficientlystable in vivo to prevent significant uncoupling prior to delivery tothe target cell. In one embodiment, the delivery complex is cleavablesuch that the ODN is released in a functional form at the target cells.

B. Pharmaceutical Compositions

The suppressive ODNs described herein may be formulated in a variety ofways depending on the location and type of disease to be treated.Pharmaceutical compositions are thus provided for both local (e.g.topical or intra-articular) use as well as for systemic use. Therefore,the disclosure includes within its scope pharmaceutical compositionscomprising at least one suppressive ODN formulated for use in human orveterinary medicine.

Pharmaceutical compositions that include at least one suppressive ODN asdescribed herein as an active ingredient, or that include both asuppressive ODN and an additional anti-inflammatory or anti-arthritisfactor as active ingredients, may be formulated with an appropriatesolid or liquid carrier, depending upon the particular mode ofadministration chosen. Additional active ingredients include, forexample, non-steroidal anti-inflammatory agents, such as diclofenac,diflunisal, etodolac, flurbiprofen, ibuprofen, indomethacin, ketoprofen,ketorolac, nabumetone, naproxen, oxaprozin, piroxicam, sulindac,tolmetin, celecoxib, and rofecoxib, steroids, such as cortisone,dexamethasone, hydrocortisone, methylprednisolone, prednisolone,prednisone, and triamcinolone, and immunosuppressives, for examplecyclosporin, tacrolimus, mycophenolic acid, and sirolimus.

The pharmaceutically acceptable carriers and excipients useful in thisdisclosure are conventional. For instance, parenteral formulationsusually comprise injectable fluids that are pharmaceutically andphysiologically acceptable fluid vehicles such as water, physiologicalsaline, other balanced salt solutions, aqueous dextrose, glycerol or thelike. Excipients that can be included are, for instance, proteins, suchas human serum albumin or plasma preparations. If desired, thepharmaceutical composition to be administered may also contain minoramounts of non-toxic auxiliary substances, such as wetting oremulsifying agents, preservatives, and pH buffering agents and the like,for example sodium acetate or sorbitan monolaurate.

The dosage form of the pharmaceutical composition will be determined bythe mode of administration chosen. For instance, in addition toinjectable fluids, topical and oral formulations can be employed.Topical preparations can include eye drops, ointments, sprays and thelike. Oral formulations may be liquid (e.g., syrups, solutions, orsuspensions), or solid (e.g., powders, pills, tablets, or capsules). Forsolid compositions, conventional non-toxic solid carriers can includepharmaceutical grades of mannitol, lactose, starch, or magnesiumstearate. Actual methods of preparing such dosage forms are known, orwill be apparent, to those of ordinary skill in the art.

The pharmaceutical compositions that comprise a suppressive ODN, in someembodiments, will be formulated in unit dosage form, suitable forindividual administration of precise dosages. The amount of activecompound(s) administered will be dependent on the subject being treated,the severity of the affliction, and the manner of administration, and isbest left to the judgment of the prescribing clinician. Within thesebounds, the formulation to be administered will contain a quantity ofthe active component(s) in amounts effective to achieve the desiredeffect in the subject being treated.

C. Therapeutic Uses

A method is disclosed herein for treating or preventing an immunemediated disorder in a subject. In one specific, non-limiting example,the immune mediated disorder is an autoimmune disease. In anotherspecific, non-limiting example, the immune mediated disorder is anallergic reaction. In a further specific, non-limiting example, theimmune mediated disorder is transplant rejection.

Autoimmune diseases include, but are not limited to inflammatoryarthritis, Hashimoto's thyroiditis, pernicious anemia, Addison'sdisease, type I diabetes, systemic lupus erythematosus, dermatomyositis,Sjogren's syndrome, dermatomyositis, lupus erythematosus, multiplesclerosis, myasthenia gravis, Reiter's syndrome, and Grave.s disease,among others.

Rejection of transplanted organs and tissues are a further example of anundesired consequence of normal immunity, which can often result indamage to and/or rejection of the transplant. Tissue rejection, alsocalled graft-versus-host disease, is a consequence of organ or tissuetransplantation caused by the transplant recipient's (host's) immuneresponse to the transplanted organ/tissue which can damage or destroyit. Ordinarily, the immune response protects the body from potentiallyharmful substances (antigens) such as microorganisms, toxins, and cancercells. The immune system distinguishes “self” from “foreign” by reactingto proteins on the surfaces of cells. It reacts against substances itrecognizes as foreign (antigens). The presence of foreign blood ortissue in the body triggers an immune response that can result in bloodtransfusion reactions and transplant rejection when antibodies areformed against foreign antigens on the transplanted or transfusedmaterial. Before transplant, tissue is “typed” according to the antigensit contains (Histocompatibility antigens).

No two people (except identical twins) have identical tissue antigens.Therefore, in the absence of immunosuppressive drugs, organ and tissuetransplantation would almost always causes an immune response againstthe foreign tissue (rejection), which would result in destruction of thetransplant. Though tissue typing ensures that the organ or tissue is assimilar as possible to the tissues of the recipient, unless the donor isan identical twin, no match is perfect and the possibility oforgan/tissue rejection remains. Immunosuppressive therapy is used toprevent organ rejection.

Allergy is another example of an immune-mediated disorder. An allergy isa collection of symptoms caused by an exaggerated immune response orreaction to substances that do not trigger an immune response in mostpeople. The term “allergy” has become synonymous with Type Ihypersensitivity (IgE-mediated allergy). Four different types ofhypersensitivity were described by Coomb and Gell (Types I, II, III andIV), as a pedagogical way to increase the understanding of differentimmune reactions which could be provoked by many antigens. In practicethese types do not necessarily occur in isolation from each other.

Allergic diseases generally begin in childhood, although they can ariseat any age. Development of allergic disease is associated with anallergic constitution due to heredity and to environmental and healthfactors. An allergic response involves an increased production ofallergen-specific IgE antibodies, which may lead to clinical symptomssuch as rhinitis, asthma, eczema, colic pains or diarrhea. A state ofhyperreactivity often accompanies an allergic reaction. If thishyperreactivity occurs in the respiratory tract, everyday stimuli likedust, tobacco smoke, cold air and perfumes may lead to allergy-likesymptoms.

The method includes administering a therapeutically effective amount ofthe suppressive ODN to a subject having or at risk of developing animmune-mediated disorder, thereby treating or preventing theimmune-mediated disorder. In one embodiment, the suppressive ODN can beadministered locally, such as by intra-articular injection. In anotherembodiment, the suppressive ODN is administered systemically. In oneembodiment, the immune-mediated disorder is an autoimmune disease, anallergy, or graft-versus-host disease. In particular embodiments, theimmune-mediated disorder is an inflammatory arthropathy.

In order to treat or prevent an immune-mediated disorder, atherapeutically effective amount of a suppressive ODN (see above) isadministered to the subject. In one embodiment, the ODN has a CD valueof greater than about 2.9, 3.0, 3.2, 3.4, 3.6, 3.8, 4.0, or 5.0. In someembodiments of the method, the ODN is from about 8 to about 120nucleotides in length. In particular examples of the method, the ODN isfrom about 10 to about 30 nucleotides in length. Optionally, thesuppressive ODN has multiple guanosine-rich sequences, for example, incertain embodiments of the method, the ODN has from about two to about20 guanosine-rich sequences, or, more particularly, from about two toabout four guanosine-rich sequences.

In some examples of the method, the ODN has at least one TTAGGG motif,and in certain examples, the ODN has multiple TTAGGG motifs. Forexample, in particular examples of the method, the ODN has from abouttwo to about 20 TTAGGG motifs, or from about two to about four TTAGGGmotifs. In particular examples of the method, the ODN has a sequenceselected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ IDNO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ IDNO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ IDNO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22,SEQ ID NO: 23, SEQ ID NO: 24, and SEQ ID NO: 25.

Combinations of these suppressive ODN are also of use. Thus, in oneembodiment, more than one suppressive ODN, each with a different nucleicacids sequence, are administered to the subject. In several specific,non-limiting examples, at least two, at least three, or at least foursuppressive ODN are administered to the subject.

In another embodiment, an additional anti-inflammatory agent orimmunosuppressive agent is administered in conjunction with asuppressive ODN. The administration of the anti-inflammatory agent orimmunosuppressive agent and the suppressive ODN can be sequential orsimultaneous.

In particular examples, the immunosuppressive agent is a non-steroidalanti-inflammatory agent, such as diclofenac, diflunisal, etodolac,flurbiprofen, ibuprofen, indomethacin, ketoprofen, ketorolac,nabumetone, naproxen, oxaprozin, piroxicam, sulindac, tolmetin,celecoxib, or rofecoxib, a steroid, such as cortisone, dexamethasone,hydrocortisone, methylprednisolone, prednisolone, prednisone, ortriamcinolone, or an immunosuppressive agent, for example cyclosporin,tacrolimus, mycophenolic acid, or sirolimus.

In another embodiment an additional anti-inflammatory agent isadministered in conjunction with a suppressive ODN. The agent can be animmunosuppressive, or an anti-arthritis agent. The administration of theanti-inflammatory agent and the suppressive ODN can be sequential orsimultaneous.

In particular examples, the immunosuppressive agent is a biologicalresponse modifier, such as Kineret® (anakinra), Enbrel® (etanercept), orRemicade® (infliximab), a disease-modifying antirheumatic drug (DMARD),such as Arava® (leflunomide), a nonsteroidal anti-inflammatory drug(NSAIDs), specifically a Cyclo-Oxygenase-2 (COX-2) inhibitor, such asCelebrex® (celecoxib) and Vioxx® (rofecoxib), or another product, suchas Hyalgan® (hyaluronan) and Synvisc® (hylan G-F20).

Thus, the suppressive ODNs disclosed herein may be administered to asubject for the treatment of immune-mediated disorders in thatindividual. ODN administration can be systemic or local. Localadministration of the ODN is performed by methods well known to thoseskilled in the art. By way of example, one method of administration tothe knee, hip and/or shoulder of an individual is by intra-articularinjection. For administration to the knee, for example, the joint to beinjected is washed with a betadine solution or other antiseptic. Asolution of about one percent lidocaine hydrochloride is injected intothe skin and subcutaneous tissue. A 3-way stopcock/needle assembly isutilized to administer the compound via an 18-30 gauge needle. The ODNis injected into the joint space using a standard lateral approach wellknown to those skilled in the art. The needle and needle tract arecleansed by flushing with 1% lidocaine hydrochloride through the 3-waystopcock assembly as the needle is withdrawn. The knee is then movedthrough a flexion-extension arc and then immobilized in full extension.The patient is then confined to bed for approximately 24 hours tominimize movement and minimize leakage of ODN from the joint.

In other embodiment, the administration of the suppressive ODN issystemic. Oral, intravenous, intra-arterial, subcutaneous,intra-peritoneal, intra-muscular, and even rectal administration iscontemplated.

In other embodiments, the method is a method of treating or preventingan autoimmune disease in a subject that involves contacting immune cellswith a suppressive ODN, and transferring the immune cells to a subjecthaving or at risk of developing an autoimmune disease, thereby treatingor preventing the autoimmune disease. Without being bound by theory,these immune cells act to suppress immune activation in a subject. Onespecific, non-limiting example is dendritic cells. Thus, in certainexamples, the immune cells, such as dendritic cells, are contacted witha suppressive ODN, and subsequently administered to a subject. Theimmune cells can be delivered alone, in conjunction with a suppressiveODN, and/or in conjunction with an additional immunosuppressive agent.The immune cells can be delivered either systemically or locally. Inseveral specific, non-limiting examples, the cells are deliveredparenterally, intravenously, intra-muscularly, sub-cutaneously, orintra-articularly.

Precise, effective quantities of cells can be readily determined bythose who are skilled in the art and will depend, of course, upon theexact condition being treated by the particular therapy being employed.The cells can be transplanted to a desired location, or can beadministered intravenously. Other agents, such as growth factors orimmunosuppressive agents, can be administered in conjunction with theimmune cells.

In other embodiments, suppressive ODNs are used to inhibit angiogenesis.In one embodiment, suppressive ODNs are utilized to inhibit angiogenesisin vivo. Thus, a suppressive ODN and a pharmacologically acceptablecarrier are administered to a subject, such that angiogenesis isinhibited in the subject. Suitable subjects include, but are not limitedto, subjects with a tumor, subjects with macular degeneration, orsubjects with diabetic retinopathy. Suitable tumors include, but are notlimited to bone, brain, breast, gastrointestinal, endocrine, eye,genitourinary, germ cell, gynecologic, head, neck, hematologic,leukemic, lung, lymphm, musculoskeletal, neurologic, respiratory,thoracic, and skin tumors.

In another embodiment, the CpG ODN is administered with a secondanti-angiogenic factor. Specific, non-limiting examples ofanti-angiogenic factors of use include, but are not limited to Macugen,rhuFab, alpha-interferon, thalidomide and prinomastat. The secondanti-angiogenic agent can be administered simultaneously or sequentiallywith the suppressive ODN.

D. Kits

Further embodiments of the disclosure include kits useful foradministering the suppressive ODN described herein in vivo or in vitro.For example, a kit useful for treating a subject with an autoimmunedisease would comprise an appropriate dosage of suppressive ODN, as wellas, optionally, any agents useful for enhancing the inhibitory effect ofsuppressive ODN. Other embodiments further include instructions forusing the kit, and/or pre-filled syringes for administering the ODN to asubject.

Thus, in one embodiment, a kit is provided including a container ofsuppressive ODN (a sufficient amount for either a single use or multipleuses), and instructions the suppressive ODN. The instructions can be inwritten form, or can be provided in an electronic format, such as on adiskette or a CD-ROM. Instructions can also be provided in the form of avideo cassette.

The subject matter of the present disclosure is further illustrated bythe following non-limiting Examples.

EXAMPLES Example 1 Repetitive Elements Present in Mammalian TelomeresSuppress Bacterial DNA-Induced Immune Activation

This example demonstrates the ability of TTAGGG multimers to inhibitCpG-induced immune activation.

A. General Methods

Reagents

Endotoxin-free phosphorothioate or phosphodiester ODNs were synthesizedat the CBER core facility. 7-DG modified ODNs were synthesized using the10-camphorsulphonyl-oxaziridine oxidization protocol recommended by themanufacturer (Glen Research, Sterling, Va.). Mammalian DNA was isolatedfrom calf thymus and murine spleen (Wizard Genomic DNA purification kit,Promega, Madison, Wis.). E. coli was obtained from Sigma (St. Louis,Mo.). Telomerase knockout mice were provided by Dr. Carol Greider (JohnsHopkins Univ., Baltimore, Md.). All DNA obtained from commercialproviders was re-purified to eliminate endotoxin (<0.1 U/mg). Doublestranded DNA was converted to single stranded DNA by heat denaturing at95° C. for 5′ followed by cooling on ice. BAL-31 (New England Biolabs,Beverly, Mass.) digestion of CT DNA was continued for 2 h at 30° C.according to manufacturer's recommendations. At the end of theincubation, the enzyme was inactivated at 65° C. for 10 min. Plasmidencoding for 1.6 kb long TTAGGG repeat was a generous gift from Dr.Jerry Shay (University of Texas Southwestern Medical Center, Dallas,Tex.). Non-telomere coding plasmid was from Vical (San Diego, Calif.).

Mice

Specific pathogen-free male BALB/c mice (Jackson Laboratories, BarHarbor, Me.) were housed in sterile micro-isolator cages in a barrierenvironment and injected i.p. with 400 g of CpG ODN plus 200 g ofsuppressive or control ODN. Spleen cells were harvested 6 h later andmonitored for cytokine production after 36 h. In order to measure thepEPO transgene expression levels, female Balb/c mice (4-6 weeks old)were injected with 30 μg of pVRmEPO (a kind gift of Vical, San Diego,Calif.) plasmid in sterile saline into the anterior tibialis musclealone or in combination with 50 μg of control or suppressive ODN.Hematocrits were measured as described (Tripathy et al., Proc Natl AcadSci USA. 93:10876-80, 1996) on blood collected by tail vein puncture.

Cytokine and IgM ELISA Assays

Immulon 2 microtiter plates (Dynex Technologies Inc., Chantilly Va.)were coated with anti-cytokine or anti-IgM antibodies (Pharmingen, SanDiego Calif.) and then blocked with PBS-1% BSA. Serially diluted culturesupernatant or serum was added for 2 h. Cytokine was detected usingbiotinylated anti-cytokine Ab followed by phosphatase-streptavidin(Pharmingen) whereas bound IgM was detected using phosphatase-conjugatedanti-IgM antibodies (Southern Biotechnology Associates, Birmingham,Ala.) as described.

Detection of Co-stimulatory Molecule Expression by FACS

2×10⁶ spleen cells/ml were incubated with ODN for 24 h. Cells werewashed, fixed with 5% paraformaldehyde for 15 min, and stained withPE-labeled anti CD-40, anti CD-86, and anti ICAM-1 (Pharmingen, SanDiego, Calif.) for 30 min at RT. Cells were washed, re-suspended inPBS/BSA (supplemented with Azide), and analyzed by FACSort (BectonDickinson, San Jose, Calif.).

Cytokine RT-PCR

Spleen cells were isolated 6 h after CpG ODN injection. Total RNA wasextracted, reverse-transcribed, and amplified in a standard PCR reactionfor 24 cycles using primers specific for murine IL-6, IL-12, and IFN aspreviously described (Takeshita et al., Neuroreport (2001)). PCRamplified material was separated on 1.5 agarose gels and visualizedunder UV light after ethidium bromide staining.

Cell Transfection and Luciferase Assay

HEK 293 (5×10⁴) cells (ATCC, Manassas, Va.) were transfected with 0.8 μgof vector plasmid (pCIneo, Promega, Madison, Wis.), pClneo-mTLR9, plus0.1 μg of p5xNF-kB-luc (Stratagene, Lajolla, Calif.) and 0.1 μg ofpSV-beta-galactosidase (Promega) and incubated overnight at 37° C. Thecells were then stimulated with indicated ODN for 24 h. Cells were thenharvested and luciferase assay was performed as recommended by themanufacturer (Promega). Beta-galactosidase activity was used tonormalize the data.

Measurement of Circular Dichroism

A Jasco J-720A spectropolarimeter was used to measure the circulardichroism of ODN (50 g/ml in 0.1×PBS). Data is expressed as the meanpeak ellipticity (mdeg/abs) of 5-10 readings/sample in the 260-270 nmrange.

Statistical Analysis

In vitro assays were performed in triplicate on at least 3 differentspleen cell preparations. All in vivo experiments were performed on aminimum of 5-10 mice/group. Statistical significance was evaluated usingStudent's t test. Correlation analysis is computed by linear correlationanalysis between CD data vs % suppression.

B. TTAGGG Multimers Inhibit CpG-induced Immune Activation

The ability of TTAGGG multimers to inhibit CpG-induced immune activationwas tested. Initial experiments showed that ODNs containing suppressivemotifs inhibit CpG-induced immune activation in a dose-dependent fashion(FIG. 2A).

ODNs containing the largest number of TTAGGG repeats (n=4) were the mostsuppressive (p<0.001; FIG. 2B). Single TTAGGG hexamers were suppressiveonly when incorporated into larger ODNs (>10 bases in length), and weresomewhat less active than TTAGGG multimers. TTAGGG motifs weresuppressive both in cis and in trans, i.e., they inhibited immuneactivation when present on the same or on a different strand of DNA thanthat expressing the stimulatory CpG sequence (FIGS. 2C and D). Thisinhibitory activity was exquisitely specific: even high concentrationsof suppressive ODNs had no effect on mitogen-induced immune responses(FIG. 2D), indicating that suppressive ODN were neither toxic nornon-specifically immunosuppressive.

C. Suppression is Mediated by Poly-G Sequences

The bases contributing to this suppressive activity were identified bysystematically modifying ODNs containing single TTAGGG motifs.Substitutions outside the telomere-derived sequence did notsignificantly affect suppression. Replacing multiple bases in the TTAregion of the TTAGGG motif also had little effect on the suppressiveactivity (FIG. 2E). In contrast, replacing two or more of the Gs in thismotif substantially reduced the ODN's ability to block CpG-inducedimmune activation (FIG. 2E). These results suggest that suppression ismediated by the poly-G sequence itself, or the two-dimensional structureimposed by that sequence.

D. Suppression is Mediated by the Two-dimensional Structure of theMotifs

To differentiate between these alternatives, individual Gs were replacedby 7-deaza guanosine (7-DG) analogues. These 7-DG substitutions did notalter the base sequence of the ODN but did prevent Hoogsteen hydrogenbonding between guanosines, thereby reducing G tetrad formation (Hurleyet al., Trends Pharmacol. Sci. 21:136-142, 2000; Lilley et al., EMBO J.13:993-1001, 1994). The resultant loss in secondary structure isreflected by a loss in circular dichroism (Lilley et al., EMBO J.13:993-1001, 1994). ODNs capable of forming G tetrads typically havepeak CD values >2, while those without such secondary structure havecircular dichroism values <1.4 (FIG. 2).

Introducing a 7-DG substitution significantly reduced an ODN's abilityto form a G-tetrad and to mediate suppression (p<0.001, FIG. 3). Toconfirm that G-tetrad formation was critical to suppression, ODNs weresynthesized that lacked the TTAGGG motif but still formed G-tetrads.These novel ODNs suppressed CpG ODN and bacterial DNA induced immunestimulation by >90% (p<0.001; FIG. 2F). Indeed, there was a consistentcorrelation between G-tetrad forming ability and suppressive activity(R=0.832, FIG. 3B).

E. Mechanism of Suppressive ODN Activity

The mechanism by which suppressive ODNs inhibit immune activation wasexplored. We confirmed that both bacterial DNA and CpG ODN stimulateDNA-dependent protein kinase activity in vitro. Of particular interest,this activity was specifically blocked by TTAGGG multimers and other Gtetrad forming ODN, but not their 7-DG modified analogues. Thesefindings indicate that suppressive motifs inhibit CpG-dependentDNA-PK_(os) activation of immune cells. In contrast, suppressive ODNsdid not block the binding or internalization of CpG ODNs mediated byToll-like receptor 9.

Example 2 Effect of Suppressive ODNs on CpG-induced Immune Action

This example demonstrates the kinetics, magnitude, and nature of theimmune inhibition elicited by suppressive motifs. Previous studiesestablished that the immunostimulatory activity of CpG DNA can bereversed several hours later either by removing the stimulatory DNA oradding suppressive DNA. The same cells that interact with stimulatorymotifs also recognize suppressive motifs. When both sequence types arepresent on the same strand of DNA, recognition proceeds in a 5′->3′direction. Suppression is generally dominant over stimulation, althougha motif in the 5′ position can interfere with recognition of a motifimmediately downstream. Understanding the rules governing cellularresponses to stimulatory and suppressive motifs facilitates the designof ODN for therapeutic uses.

A. General Methods

Animals:

Female Balb/c mice were obtained from the Jackson Laboratories (BarHarbor, Me.). The mice were housed under specific pathogen freeconditions, and used at 8-20 weeks of age. All studies involvedprotocols approved by the CBER Animal Care and Use Committee.

Oligodeoxynucleotides:

Studies utilized phosphorothioate modified ODNs that were synthesized atthe CBER core facility Verthelyi, D., et al., J Immunol (2001) 166:2372.The following ODNs were used: immunostimulatory ODN1466 (TCAACGTTGA;SEQ. ID NO: 26) and ODN1555 (GCTAGACGTTAGCGT; SEQ. ID NO: 27), controlODN1471 (TCAAGCTTGA; SEQ. ID NO: 28) and ODN1612 (GCTAGAGCTTAGGCT; SEQ.ID NO: 29), suppressive ODN1502 (GAGCAAGCTGGACCTTCCAT; SEQ. ID NO: 20)and ODNH154 (CCTCAAGCTTGAGGGG; SEQ. ID NO: 1). Underlined basesrepresent the 10-mer sequences that were incorporated into complexmulti-determinant ODN used in some experiments. There was no detectableprotein or endotoxin contamination of these ODN.

Mammalian DNA was purified from BALB/c spleens (Wizard Genomic DNApurification kit, Promega, Madison, Wis.). E. coli DNA was obtained fromGibco BRL (Rockville, Md., USA). Endotoxin contamination in thesepreparations was <0.1 U/ml after purification Klinman, D. M., et al., J.Immunol. (1997) 158:3635. Double stranded DNA (dsDNA) was converted tosingle stranded DNA (ssDNA) by heat denaturing at 95° C. for 5′ followedby immediate cooling on ice.

Cytokine ELISA Assays:

Single spleen cell suspensions were washed 3 times and re-suspended inRPMI-1640 supplemented with 5% heat inactivated fetal calf serum (FCS),1.5 mM L-glutamine and 100 U/ml of penicillin/streptomycin. 5×10⁵cells/well were cultured in flat-bottomed microtiter plates (Costar,Corning, N.Y.) with 1 uM ODN for 18-24 h. Culture supernatants werecollected, and cytokine levels measured by ELISA. In brief, 96 wellImmulon H2B plates were coated with cytokine-specific antibodies andblocked with PBS1% BSA as previously described in Klinman, D. M., andNutman, T. B., Current Protocols in Immunology (1994), J. E. Coligan, A.M. Kruisbeek, D. H. Margulies, E. M. Shevach, and W. Strober, eds.,Greene Publishing Associates, Brooklyn, N.Y. Culture supernatants wereadded, and bound cytokine detected by the addition of biotin labeledsecondary antibodies followed by phosphatase-conjugated avidin and aphosphatase-specific colorimetric substrate (PNPP, Pierce, Rockford,Ill.). Standard curves were generated using recombinant cytokines. Thedetection limit for these assays was: 0.8 U/ml for IFNg, 0.1 ng/ml forIL-6 and 0.1 ng/ml for IL-12. All assays were performed in triplicate.

Cytokine-specific ELIspot Assays:

A single spleen cell suspension prepared in RPMI 1640 plus 5% FCS wasserially diluted onto plates pre-coated with anti-cytokine Abs. Klinman,D. M., and Nutman, T. B., Current Protocols in Immunology (1994), J. E.Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, and W.Strober, eds., Greene Publishing Associates, Brooklyn, N.Y. Cells wereincubated with 1 uM ODN at 37° C. for 8-12 h, and their secretion ofcytokine detected colorimetrically as previously described. Klinman, D.M., and Nutman, T. B., Current Protocols in Immunology (1994), J. E.Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, and W.Strober, eds., Greene Publishing Associates, Brooklyn, N.Y.

Cell-surface Binding and Internalization of ODN:

Spleen cells (2×106/ml) were incubated with 1 uM of unlabeled and/orfluorescent-labeled ODN for 10′ at 4° C. (binding experiments) or at 37°C. for 1 h (uptake experiments Gursel, M., et al., J. Leuko. Biol.(2001) in press. Cells were washed, fixed, and analyzed by FACScan(Becton Dickinson, San Jose, Calif.).

Statistical Analysis:

Statistically significant differences between two groups were determinedusing the Wilcoxon Rank Sum Test. When comparing more than two groups,differences were determined using a 2-tailed non-parametric ANOVA withDunn's post-test analysis. p values <0.05 were considered significant.

B. Mammalian DNA Suppresses CpG DNA-Induced Immune Activation

Single stranded bacterial DNA and synthetic ODN containing unmethylatedCpG motifs stimulate immune cells to mature, proliferate and producecytokines, chemokines, and Ig. Klinman, D. M., et al., Proc. Natl. Acad.Sci. USA (1996) 93:2879; Roman, M., et al., Nature Medicine (1997)3:849. (Roman et al., (1997) Nature Medicine 3:849; Yamamoto et al.,(1992) J. Immunol. 148:4072; Krieg et al., (1995) Nature 374:546). Theseeffects can be blocked by “poly-G” and/or “GC” rich DNA motifs (Krieg etal., (1998) Proc. Natl. Acad. Sci. 95:12631; Pisetsky et al., (1995) NYAcad. Sci. 772:152). Scores of ODNs were synthesized and tested, andeventually several were identified that selectively inhibitedCpG-induced immune responses. The two most active of these suppressiveODN (ODN1502 and ODNH154) were selected for detailed study. As seen inFIG. 4, suppressive ODN blocked a majority of the IFNγ productioninduced by bacterial DNA or CpG ODN (p<0.01). Suppressive ODN wereneither toxic nor broadly immunosuppressive, as they did not interferewith the mitogenic activity of LPS or Con A (FIG. 4).

The activity of suppressive ODNs was concentration dependent, with 50%suppression being achieved at a suppressive:CpG ODN ratio ofapproximately 1:3 (FIG. 5). To examine the kinetics of this inhibition,suppressive ODN were added to BALB/c spleen cells at various times afterCpG-induced stimulation. Maximal inhibition was observed whensuppressive ODN were co-administered with CpG ODN, althoughstatistically significant inhibition persisted when suppressive ODN wereadded up to 3 h later (FIG. 6). These findings suggest that CpG inducedimmune activation is an ongoing process, and can be inhibited after thestimulatory signal is delivered.

To test this conclusion, spleen cells were incubated with CpG ODN forvarious periods and cytokine production analyzed after 24 h. Cellsstimulated with CpG DNA for 8 h produced 90% as much cytokine as cellsstimulated continuously for 24 h (FIG. 7). Cells treated with CpG ODNfor only 4 h produced half as much cytokine, while cells treated withCpG DNA for <2 h showed only minimal activation (FIG. 7). These findingssupport the conclusion that CpG-induced cellular activation isreversible for several hours.

C. Suppressive ODNs do not Block CpG ODN Uptake or Induce the Productionof Inhibitory Factors

The results described above indicate that CpG-induced immune activationcan be reversed either by adding suppressive ODNs or by removingstimulatory ODNs. This suggests that suppressive ODNs block the ongoinguptake of CpG DNA. Yet FACS analysis demonstrated that neither cellsurface binding nor internalization of FITC-labeled CpG ODN wassignificantly reduced by suppressive ODN at concentrations that blockedcytokine production by approximately 75% (FIG. 8).

The possibility that suppressive motifs might induce the production of afactor that blocks CpG-dependent immune activation was theninvestigated. Initial studies established that BALB/c spleen cellspre-incubated with suppressive ODN remained unresponsive to CpG-inducedstimulation for several hours (Table I, line 3). If this non-responsivestate was mediated by a soluble factor (or inhibitory cell-cellinteractions) then cells pre-treated with suppressive ODN should blockCpG-induced stimulation of naive spleen. As seen in Table I, cellstreated with suppressive ODN had no significant effect on CpG dependentcytokine production by fresh splenocytes.

TABLE I Effect of mixing cells treated with suppressive versusstimulatory ODN Cells ODN added % maximal cytokine pre-treated withduring production suppressive ODN Fresh cells culture IL-6 IL-12 − + CpG100 ± 13  100 ± 6  − + Control 3 ± 2 7 ± 2 + − CpG 9 ± 6 6 ± 2 + −Control 0 ± 0 0 ± 0 + + CpG 86 ± 16 105 ± 12  + + Control 0 ± 0 0 ± 0BALB/c spleen cells were treated with 1 uM suppressive ODN₁₅₀₂ for 2 hand then washed (first column). These cells were added to naivesplenocytes (second column) plus 1 uM of control ODN₁₄₇₁ or CpG ODN₁₅₅₅.IL-6 and IL-12 levels in culture supernatants were measured by ELISAafter 18 h. Results represent the average + SD of triplicate assays,each standardized to the response induced by bacterial DNA (62 pg/mlIL-6; 134 pg/ml IL-12).D. Cellular Recognition of Suppressive Versus Stimulatory Motifs

The above studies establish that suppressive motifs on one strand of DNAblock the immune activation induced by stimulatory motifs on a differentstrand (i.e., trans suppression). To better understand the interactionbetween suppressive and stimulatory motifs, ODNs containing both weresynthesized. In the simplest case, a 20-mer was constructed in which aCpG motif was placed immediately 5′ to a suppressive motif (referred toas [CpG-Sup] ODN).

Experiments showed that this ODN was stimulatory, triggering murinespleen cells to produce IL-6, IL-12 and IFNγ to the same extent as anODN of the same length in which the suppressive motif was replaced by a‘control’ sequence (i.e., one that was neither stimulatory norsuppressive, Table II). [CpG-Sup] ODNs also failed to block the immuneactivation induced by an independent CpG ODN (Table II). These resultssuggest that a suppressive motif is inactive when located immediately 3′to a CpG motif on the same strand of DNA. Similar results were obtainedin studies of additional [CpG-Sup] ODNs that utilized differentstimulatory and suppressive motifs.

TABLE II Effect of motif position on immunostimulatory activity Locationof motifs # of cytokine secreting cells (5′ → 3′) IL-6 IL-12 IFNg CpGODN* 79 ± 13 1980 ± 230 260 ± 40 [CpG-Sup] ODN* 72 ± 14 2080 ± 480 230 ±60 [Sup-CpG] ODN 0 ± 0 140 ± 30  0 ± 0 [CpG-Cont] ODN* 64 ± 12 2210 ±130 284 ± 34 [Cont-CpG] ODN* 80 ± 11 1942 ± 88  238 ± 28 [Cont-Sup] ODN8 ± 2 184 ± 34 36 ± 8 [CpG-Sup] ODN + Sup 4 ± 2 226 ± 38 28 ± 6 ODN[Sup-CpG] ODN + CpG 7 ± 3 250 ± 32 34 ± 9 ODN* 10⁶ BALB/c spleen cellswere co-incubated with 1 uM of each ODN. Complex ODN (20 bp in length)were constructed from 10-mers containing suppressive (Sup), stimulatory(CpG) or control (Cont) motifs. The number of cytokine secretingcells/10⁶ was determined by ELIspot after 24 h of stimulation.Equivalent results were derived using combinations of motifs derivedfrom two different stimulatory (ODN₁₅₅₅ and ODN₁₄₆₆), control (ODN₁₄₇₁and ODN₁₆₁₂) and suppressive (ODN₁₅₀₂ and ODN_(H154)) ODN. Resultsrepresent the average ± SD of triplicate assays involving at least twoODN of each type. *Stimulatory ODN, p < .05.

To better understand this phenomenon, longer ODNs were synthesized inwhich the CpG and suppressive motifs were separated by progressivelylonger CT spacers. Adding a 5 base spacer generated an ODN that wasstill stimulatory (Table III). However, separating the motifs by >10bases yielded ODNs that were suppressive, since they blocked thestimulatory activity of co-administered CpG ODNs (Table III).

TABLE III Effect of distance between motifs on ODN activity Cytokineproducing cells (% maximum) ODN IL-6 IL-12 IFNg CpG ODN* 100 ± 11  100 ±7  100 ± 10  CpG ODN* + Cont ODN 97 ± 14 98 ± 9  100 ± 17  CpG ODN* +Sup ODN 16 ± 6  21 ± 6  18 ± 5  [CpG-Sup] ODN* 87 ± 12 >100 ± 14  92 ±14 [CpG-5 bases-Sup] ODN* >100 ± 4   >100 ± 21  >100 ± 22  [CpG-10bases-Sup] ODN 38 ± 6  64 ± 15 42 ± 7  [CpG-20 bases-Sup] ODN 7 ± 4 48 ±13 24 ± 8  [CpG-20 bases-Cont] ODN* 94 ± 7  >100 ± 14  99 ± 11 [Sup-CpG]ODN 0 ± 0 0 ± 0 0 ± 0 [Sup-20 bases-CpG] ODN 8 ± 5 9 ± 3 2 ± 1 [CpG-Sup]ODN* + CpG >100 ± 16  >100 ± 15  98 ± 13 ODN* [CpG-5 bases-Sup]ODN* + >100 ± 18  >100 + 11  98 ± 20 CpG ODN* [CpG-10 bases-Sup] ODN +58 ± 7  75 ± 9  66 ± 9  CpG ODN* [CpG-20 bases-Sup] ODN + 27 ± 5  26 ±10 30 ± 8  CpG ODN* [Sup-CpG] ODN + CpG 9 ± 4 11 ± 4  8 ± 5 ODN* [Sup-20CT-CpG] ODN + 5 ± 1 9 ± 3 13 ± 2  CpG ODN* BALB/c spleen cells werestimulated in vitro with 1 uM of each ODN, and the number of cellsactivated to secrete cytokine determined 8 h later by ELIspot. Thepercent of cells activated to secrete cytokine was calculated by theformula: (# of cells activated by test ODN) − (background)/(# of cellsactivated by CpG ODN) − (background) × 100%. Two different control(ODN₁₄₇₁, and ODN₁₆₁₂), CpG (ODN₁₄₆₆ and ODN₁₅₅₅) and suppressive(ODN₁₅₀₂ and ODN_(H154)) ODN gave similar results in these experiments.Results represent the average of 2-4 assays/data point. Table II showstypical numbers of cytokine secreting cells/10⁶. *Stimulatory ODN, p <.05.

The trivial possibility that the CT spacer somehow reduced CpG activitywas eliminated by substituting a “control” motif for the 3′ suppressivemotif. The resulting ODNs were fully stimulatory (Table III).

The impact of placing a suppressive motif 5′ to a CpG motif was thenexamined. ODNs with a suppressive motif in the 5′ position inducedlittle or no immune activation, even when the CpG motif was shifted upto 20 by downstream from the suppressive motif (Tables II and III). Thislack of activity could not be attributed to the 3′ location of the CpGmotif, since CpG ODNs with a ‘control’ sequence at the 5′ end wereimmunostimulatory. All ODNs containing a suppressive motif in the 5′position also inhibited co-administered CpG ODN (Tables II and III).These findings suggest that the relative position of stimulatory andsuppressive motifs determines the immunomodulatory properties of DNA.

Example 3 Suppressive ODN Permit Higher Levels of Transgene Expression

This example demonstrates that suppressive ODNs permit higher levels oftransgene to be expressed when the transgene vector containsimmunostimulatory CpG motifs.

Balb/C mice were injected intramuscularly with 30 μg vector encodingerythropoietin alone or together with 50 μg of each suppressive ODN.Suppressive ODN was either co-injected at the time of vector injectionor was given 3 days prior to vector injection. Transgene expression wasstudied by measuring the hematocrit levels from blood at variousintervals. Data represent mean+S.D. for three animals. Suppressive ODNpermitted higher levels of transgene expression (FIG. 9).

Without being bound by theory, it is believed that this increase intransgene expression is limited by immune activation triggered byimmunostimulatory CpG motifs in the erythropoietin construct.Administration of suppressive ODN inhibits this immune activation andpermits the transgene to be expressed at higher levels.

Example 4 Suppressive ODN Blocks the Activity of CpG Motifs In Vivo

This example shows that suppressive ODNs work in vivo to directlycounteract the activity of immunostimulatory CpG motifs.

The effect of Suppressive ODN on CpG ODN-induced immune protection wasstudied. Balb/c mice were injected IP with 50 μg of each ODN. Five dayslater, animals were challenged IP with 10³ LD50 of Listeriamonocytogenes. Survival was monitored for >3 weeks, although all animalsthat succumbed to infection died within one week of challenge.Suppressive ODN blocked the activity of CpG motifs in vivo (FIG. 10).

Example 5 Reduction of CpG-Induced Arthritis by SuppressiveOligodeoxynucleotides

This example demonstrates the influence of CpG DNA and suppressive ODNson the propensity of the host to develop arthritis, and indicates thatthe mechanism of suppressive ODN action is mediated by Cd11c positivecells.

A. General Methods

Animals:

Female BALB/c mice were obtained from the Jackson Laboratories (BarHarbor, Me.). ACUC approved studies were conducted using 8-20 week oldmice.

Oligodeoxynucleotides:

ODNs were synthesized at the CBER Core Facility. Sequences of thephosphorothioate ODN used were:

(SEQ ID NO: 30) CpG: GCTAGACGTTAGCGT (SEQ ID NO: 1) suppressive:CCTCAAGCTTGAGGGG (SEQ ID NO: 31) control: GCTAGATGTTAGCGT.All ODN were free of detectable protein or endotoxin contamination.Experimental Protocol:

25 g of ODN in 6 μl of PBS was injected into the knee joint using a 30gauge needle. In some studies, knees were re-injected with PBS or 25 μgof suppressive ODN 24-48 h after initial CpG ODN administration. Jointswelling was measured in the coronal plane using a micrometer caliper.Histologic analysis was performed by a blinded investigator on fixed,decalcified and paraffin embedded sections stained withhematoxylin/eosin.

TNFα Assays:

Single spleen cell suspensions were prepared in RPMI-1640 supplementedwith 5% heat inactivated fetal calf serum, 1.5 mM L-glutamine and 100U/ml of penicillin/streptomycin. 5×10⁵ cells/well were cultured inflat-bottomed microtiter plates (Costar, Corning, N.Y.) with ODN for 72hr. TNFα levels in culture supernatants were measured by ELISA. Inbrief, 96-well Immulon H2B plates were coated with anti-TNFα Ab(Genzyme, Cambridge, Mass.). Plates were blocked with PBS-1% BSA andoverlaid with culture supernatants. Bound cytokine was detected by theaddition of biotin labeled anti-TNFα Ab (Genzyme, Cambridge, Mass.)followed by phosphatase-conjugate avidin.

RT-PCR:

Total RNA was extracted from homogenized knees using TRIzol reagent(GibCO Life Technologies, Gaithersburg, Md.) as recommended by themanufacturer. 5 ug of total RNA was reverse transcribed into cDNA, whichwas assayed for TNFα (sense ATGAGCACAGAAAGCATGATC, antisenseTACAGGCTTGTCACTCGAATT, 275 bp) and β-actin (senseGACATGGAGGAGTCTGGCACCACA, antisense ATCTCCTGCTCGAAGTCTAGAGCAA, 440 bp)by PCR as previously described (Takeshita et al., Neuroreport (2001)12:3029-3032). Relative band intensity was determined by ethidiumbromide staining of 1% agarose gels using NIH-Image software.

Statistical Analysis:

Statistically significant differences between two groups were determinedusing the Wilcoxon Rank Sum Test. When comparing more than two groups, atwo-tailed non-parametric ANOVA with Dunn's post-test analysis was used.Differences in joint diameters were analyzed by repeated-measures ANOVAusing the Proc Mixed procedure from the Statistical Analysis System(SAS). p values <0.05 were considered significant.

B. Induction of Arthritis by CpG ODN

Microbial infection of the gastrointestinal (GI) or genitourinary (GU)tracts is associated with the development of reactive arthritis inhumans. Evidence suggests that bacterial DNA contributes to thisprocess, since 1) bacterial DNA can be detected in arthritic joints(Braun et al., J. Rheumatol. (2000) 27:2185-2192), and 2) bacterial DNAinduces joint inflammation when injected into the knees of normal mice(Deng et al., Nat. Med. (1999) 5:702-705). Deng et al. established thatimmunostimulatory CpG motifs were the cause of this inflammation byshowing that CpG-containing oligodeoxynucleotides (ODN) induced diseasein a manner similar to that induced by purified bacterial DNA (Deng etal., supra). This effect is consistent with the proinflammatoryproperties of CpG ODN, including their ability to stimulate immune cellsto proliferate, differentiate, and secrete proinflammatory chemokinesand cytokines (Deng et al., supra; Klinman et al., Springer Semin.Immunopathol. (2000) 22:173-83).

Consistent with the findings of Deng et al. (Deng et al., ArthritisRheum. (2000) 43:356-364), BALB/c knees injected with CpG ODN developedinflammatory arthritis within 24 hr that peaked after 3-7 days (FIG.11). CpG-induced arthritis was characterized by swelling (0.14+0.04 mmvs 0.02+0.02, p=0.054) and histological changes that includedperivascular infiltration by mononuclear cells and hyperplasia of thesynovial lining (FIG. 11). These inflammatory effects were CpG-specificand localized, since no disease was observed in contra-lateral kneesinjected with PBS or control ODN. Similar swelling and histologicchanges were observed in knees injected with bacterial DNA.

C. Suppressive ODN Block the Development of CpG-induced Arthritis

To determine whether suppressive ODN prevent CpG mediated inflammatoryarthritis, knees were co-injected with 25 g of suppressive plus 25 g ofCpG ODN. The inclusion of suppressive ODN reduced swelling from0.14+0.04 mm to 0.02+0.02 mm (p=0.004) and the inflammatory score from1.94+0.32 to 0.67+0.12 (p=0.018, FIG. 11). When joint inflammation wasassessed by magnetic resonance imaging, suppressive ODN reduced CpG ODNinduced fluid accumulation from 95.4+8.2 MR-signal intensity units to52.3+6.7 units (n=5, p<0.001). These effects were specific, sinceco-administering PBS or control ODN had no impact on CpG-inducedarthritis (FIG. 11). In parallel studies, suppressive ODN prevented thearthritis induced by bacterial DNA but not LPS (data not shown).

D. Kinetics of the ODN Anti-inflammatory Effect

To examine the kinetics of this anti-inflammatory effect, suppressiveODN were administered 0, 24 and 48 h after CpG ODN injection. To controlfor the effect of multiple injections, the contralateral knee wasinjected with PBS, and the difference in swelling between the two jointsevaluated daily. A significant reduction in swelling was observed whenjoints were treated with suppressive ODN up to two days after CpGadministration (p=0.012, FIG. 11C). However, maximal control ofarthritis required early intervention (p=0.011, D0 vs D2).

E. Suppressive ODNs Reduce Intra-articular TNF Production

Previous studies established that the magnitude of CpG-induced arthritiscorrelated with intra-articular TNFα levels (Deng et al., Arthritis Res.(2001) 3:48-53). Consistent with TNFα playing a critical role in thedisease process, TNFα KO mice fail to develop CpG-induced arthritis(Deng et al., Arthritis Rheum. (2000) 43:356-364; Ronaghy et al., J.Immunology (2002) 168:51-56). To evaluate whether suppressive ODN had aneffect on TNFα production, BALB/c spleen cells were stimulated in vitrowith CpG+suppressive ODN. As seen in FIG. 12, suppressive ODN reducedTNFα production in a dose-dependent manner, whereas control ODN had noeffect.

To monitor the in vivo effect of suppressive ODN on TNF production,cytokine mRNA levels were measured in the joint. Consistent with earlierreports (Deng et al., Arthritis Rheum. (2000) 43:356-364; Ronaghy etal., J. Immunology (2002) 168:51-56; Kyburz et al., Arthritis Rheum.(2001) 44 (Suppl): S396), CpG ODN up-regulated local TNF mRNA levels(FIG. 12C, D). Co-administering suppressive ODN reduced TNFα mRNAby >50% (p<0.003, FIG. 12).

Example 6

Systemic Effect of Stimulatory and Suppressive Oligodeoxynucleotides onthe Induction of Inflammatory Arthritis

A. General Methods

Animals:

Female BALB/c mice were obtained from the Jackson Laboratories (BarHarbor, Me.). The mice were used at 8-20 weeks of age and were housedunder specific pathogen free conditions. All experiments were approvedby the CBER Animal Use and Care Committee.

Oligonucleotides:

ODN used in this study had a phosphorothioate backbone, and weresynthesized in the CBER Core Facility. They contained <0.1 EU ofendotoxin per mg of ODN, as assessed by a Limulus amebocyte lysate assay(QCL-1000, BioWhittaker). The sequence of the CpG ODN wasGCTAGACGTTAGCGT (SEQ. ID NO: 30), of the suppressive ODN:CCTCAAGCTTGAGGGG (SEQ. ID NO: 1), and of the control ODN:GCTAGATGTTAGCGT (SEQ. ID NO: 31).

Experimental Protocols:

Arthritis was induced as previously described in Zeuner, R A, et al.,Arthritis Rheum. (2002), in press. Briefly 1 or 25 μg of ODN in 6 μl ofPBS was injected into the knee joint using a 30 gauge needle. Jointswelling was measured in the coronal plane using a micrometer caliper(General Tools Mfg CO, NY, N.Y.). Mice were euthanized on day 4 and theknees fixed, decalcified, sectioned, and stained with hematoxylin/eosinprior to histologic examination. Scoring was performed by a blindedinvestigator using a scale of 0-4. 0=absence of inflammation, 1=sparse,localized perivascular infiltrate, 2=moderate infiltrate,3=moderate-dense infiltrate with synovial hyperplasia, 4=denseinfiltrate with pronounced synovial hyperplasia.

In some experiments, donor mice were injected IP with 300 μg of ODN inPBS. A single cell suspension prepared from the spleens of these micewas prepared, and 20×106 transferred IV to naive littermate recipients.These spleen cells were enriched or depleted of various subpopulationsusing magnetic bead separation (Vario-Macs System, Miltenyi) asrecommended by the manufacturer.

Statistical Analysis:

Differences between two groups determined using the Wilcoxon Rank SumTest. Differences between multiple groups were evaluated using atwo-tailed

ANOVA on Ranks with Dunn's post test analysis. Differences in jointdiameters were compared by repeated-measures ANOVA. P values <0.05 wereconsidered significant. Data are presented as mean+SEM.F.

B. Effect of Systemic CpG ODN on Sensitivity of Joints to InflammatoryStimuli

Previous studies established that intra-articular injection of bacterialDNA or CpG ODN induces arthritis in mice, characterized by aninflammatory cell infiltrate, perivascular accumulation of mononuclearcells, and hyperplasia of the synovial lining Deng, G M, and TarkowskiA., Arthritis Rheum. (2000) 43:356-364. Since reactive arthritis inhumans is associated with infection of the GI or GU tract rather thanthe joint, we explored whether CpG DNA in the systemic circulation mightalter the sensitivity of joints to inflammatory stimuli.

To examine this possibility, normal BALB/c mice were injected IP with300 ug of CpG DNA, and then challenged with a sub-arthritogenic dose oflocal CpG ODN. As seen in FIG. 14, normal mice and mice treated with PBSor control ODN did not develop arthritis (no inflammation, no swelling)when injected with 1 μg of CpG. In contrast, animals pre-treated withsystemic CpG DNA developed significant joint swelling, a mononuclearcell infiltrate, and synovial hyperplasia when challenged with the samedose of CpG ODN. These changes were triggered by exposure to local CpGDNA, as no inflammation developed when the joints of systemicallytreated animals were injected with PBS.

These findings indicate that CpG DNA in the systemic circulation(perhaps released by dying bacteria in the GI or GU tract) can increasethe host's susceptibility to the development local arthritis.

C. Systemic Administration of Suppressive ODN Reduces Susceptibility toArthritis

It has been demonstrated that suppressive ODN (containing motifs thatselectively inhibit the immunostimulatory activity of CpG ODN)significantly reduce the swelling, synovial hyperplasia and leukocyteinfiltration induced by CpG DNA. These effects were observed whensuppressive ODN were injected directly into arthritic joints. Based onthe observation that systemic CpG DNA can increase the host'ssusceptibility to arthritis, we postulated that suppressive ODN in thesystemic circulation might lower this susceptibility.

To test this hypothesis, BALB/c mice were treated IP with 300 ug ofsuppressive ODN 0-3 days prior to the intra-articular injection of 25 ugCpG DNA. Consistent with previous studies, naive mice (and micepre-treated with control ODN or PBS) developed severe arthritisfollowing local CpG ODN challenge (FIG. 15). In contrast, systemicadministration of suppressive ODN three days prior to local CpG DNAchallenge reduced joint swelling and inflammation by 80-85% (FIG. 16;p<0.029). Unlike the situation with locally administered suppressiveODN, which reduced inflammation when administered up to 2 days after theinduction of arthritis, suppressive ODN were effective systemically onlyif delivered several days prior to the induction of arthritis. Thesefindings suggest that instead of blocking CpG induced arthritis locally,suppressive ODN in the systemic circulation might activate a regulatorycascade that requires several days to mature.

D. Spleen Cells from Suppressive ODN Treated Mice Prevent CpG-inducedArthritis

To investigate this possibility, spleen cells from mice treatedsystemically with suppressive ODN were transferred to naive controls,which were then injected with 25 ug of CpG DNA intra-articularly. Asexpected, spleen cells from untreated donors had no effect on thedevelopment of CpG-induced arthritis (FIG. 17). By comparison, thetransfer of 20×10⁶ spleen cells from suppressive ODN treated donorssignificantly reduced joint swelling and inflammation in the recipients.These findings indicate that systemically administered suppressive ODNelicit a population of regulatory cells that inhibit CpG-inducedarthritis.

To define the time course over which these regulatory cells aregenerated, splenocytes were isolated from 1-3 days after treatment withsuppressive ODN. Cells from animals treated with suppressive ODN for 3days significantly inhibited CpG-induced arthritis, whereas splenocytesfrom animals exposed to suppressive ODN for shorter periods wereprogressively less effective.

To characterize the cell type responsible for this resistance toCpG-induced arthritis, magnetic beads were used to deplete or enrichspecific cell subpopulations from donor spleens. Depletion of CD19+ Bcells, T cells, or NK cells had no effect on CpG-induced arthritis (FIG.18). However, removal of CD11c+ dendritic cells resulted in a completeabrogation of the suppressive activity of the transferred spleen cellpopulation. Similarly, the transfer of only 5×105 CD11c+ enriched cellsfrom suppressive ODN treated mice to normal recipients conferredresistance to CpG-induced arthritis.

Example 7 Neutralizing ODN Inhibits HSV DNA-Induced Angiogenesis

A. General Methods

Phosphorothioate ODNs were synthesized at the Center for BiologicsEvaluation and Research Core Facility, as described (Verthelyi et al.,(2001) J. Immunol. 166, 2372-2377). The sequences of the stimulatoryODNs used in this study were: 1466, TCAACGTTGA (SEQ. ID NO: 26), and1555, GCTAGACGTTAGCGT (SEQ ID No: 27); subsequent studies were conductedusing an equimolar mixture of ODNs 1466 and 1555), the control ODN 1471has the sequence TCAAGCTTGA (SEQ ID NO: 28), and the neutralizing ODNhas the sequence GAGCAAGCTGGACCTTCCAT (SEQ ID NO: 20). There was nodetectable endotoxin contamination in any of the ODNs, as monitored byLimulus amebocyte lysate assay (BioWhittaker). In some experiments, FITCwas conjugated to the 5′ end of these ODN to monitor their distributionin vivo.

Herring sperm DNA (Boehringer Mannheim) was prepared by passage throughDetoxi-Gel Endotoxin Removal Gel 20344 (Pierce) to reduce endotoxinlevels to <6 endotoxin units per mg. Recombinant human VEGF165 (rhVEGF),recombinant mouse VEGF (rmVEGF), mouse VEGF-neutralizing antibody, andbiotinylated rat anti-mouse VEGF were purchased from R & D Systems.Synthetic mesh and hydron polymer (type NCC) were purchased from SefarAmerica (Kansas City, Mo.) and Hydro Med Sciences (Cranbury, N.J.),respectively. Sucralfate was kindly provided by Bulch Meditec (Vaerlose,Denmark). Lipopolysaccharide was purchased from Sigma, andstreptavidin-PE from PharMingen.

Isolation of HSV-1 DNA

Virus was harvested from infected Vero cells when the cytopathic effectswere maximal, as described (Killington et al., (1996) in VirologyMethods Manual, eds. Mahy, B. W. J. & Kangro, H. O. (Academic, NewYork), pp. 71-88; McCance, D. J. (1996) in Virology Methods Manual, eds.Mahy, B. W. J. & Kangro, H. O. (Academic, New York), pp. 191-197). Cellswere suspended in sterile PBS and freeze-thawed three times to releaseviral particles. The virion-containing supernatant was thenultracentrifuged at 25,000×g for 90 min at 4° C., and the pelletsuspended in sterile PBS. Viral particles were precipitated in asolution of 7% polyethylene glycol 8000 in 2.3% NaCl overnight at 4° C.and then centrifuged at 25,000×g. DNA was isolated from virions bytreatment with 200 μg/ml proteinase K and 1% sarcosyl in STE bufferovernight at 56° C. The DNA was purified by multiplephenol/chloroform/isoamyl alcohol extractions, precipitated, sedimentedat 12,000×g, dried, and resuspended in sterile STE buffer. RNA wasremoved by incubation with RNase (100 mg/ml; 5 Prime 3 Prime) for 1 h at37° C., and the DNA reextracted as described above. The resultantmaterial provided a single band by electrophoresis and containedundetectable protein (checked spectrophotometrically) or cellular DNA(measured by PCR for -actin DNA). All procedures were performed in asterile environment, and all buffers and solutions were checked for thepresence of lipopolysaccharide by using the Pyrogent plus test. Nodetectable protein, cellular RNA, or DNA, and less than 0.06 endotoxinunits of endotoxin per mg of HSV DNA, were found.

Mice

Female BALB/c (Harlan-Sprague-Dawley) were used for all experiments.Animals were housed and cared for as described (Gangappa et al., (1998)J. Immunol. 161, 4289-4300).

Corneal Micropocket Assay

The murine corneal micropocket assay used in this work observed thegeneral protocol of Kenyon et al. (Kenyon et al., (1996) Invest.Ophthalmol. Vis. Sci. 37, 1625-1632). Pellets 0.4×0.4×0.2 mm3 composedof sucralfate and hydron polymer were prepared (Kenyon et al., (1996)Invest. Ophthalmol. Vis. Sci. 37, 1625-1632). Known amounts of VEGF,DNA, stimulatory or neutralizing ODN, and/or combinations thereof wereadded to these pellets before insertion into corneal pockets. Themicropockets were placed 0.6-0.8 mm from the limbus (in the pericenterof the cornea at the lateral canthus of the eye) under stereomicroscopy(four eyes per group). In some experiments, anti-mVEGF-neutralizingantibody (5 μg in 5 μl of PBS) was injected subconjunctivally into theeyes of recipient mice just before and 2 days after pellet implantation.

Angiogenesis was quantitated at multiple times after pellet implantationunder stereomicroscopy. The length of the neovessels generated from thelimbal vessel ring toward the center of the cornea and the width of theneovessels presented in clock hours (each clock hour is equal to 30° C.at the circumference) was measured (Zheng et al., (2001) Am. J. Pathol.159, 1021-1029). The angiogenic area was calculated according to theformula for an ellipse. A=[(clock hours)×0.4×(vessel length in mm)×]/2.

Immunohistochemical Staining

Eyes were removed and snap frozen in OCT compound (Miles). Sections(6-μm) were cut, air dried, and fixed in cold acetone for 10 min. Thesections were blocked with 3% BSA and stained with biotinylatedanti-mVEGF164. Sections were then treated with horseradishperoxidase-conjugated streptavidin (1:1,000) and 3,3′-diaminobenzidine(Vector), and counterstained with hematoxylin as described (Zheng etal., (2001) J. Virol. 75, 9828-9835). Cellular infiltration wasdetermined microscopically by counting the infiltrating cells in thecorneal stroma. Each data point represents the mean total cellularinfiltrate in four central corneal sections from two eyes.

VEGF Staining of J774A.1 Cells

J774A.1 cells were plated and incubated in two-well chamber slides(Lab-Tek, Nalge Nunc International) or in 24-well plates [for laterreverse transcription (RT)-PCR] in DMEM with 10% FBS overnight at 37° C.in 5% CO2. The cells in chamber slides were cocultured with FITC-labeledCpG ODN (1555) or control ODN (1471) at a concentration of 2 μg/106cells. The cells were washed twice with PBS and fixed in a 1:1 mixtureof acetone/methyl alcohol at 20° C. for 15 min. The cells were stainedwith biotinylated rat-anti-mVEGF 6-18 h after ODN stimulation andsubsequently reacted with streptavidin-PE. Images were taken by using afluorescence microscope (Hamamatsu, Ichinocho, Japan). The cells in24-well plates were treated with 2 μg of ODN per 106 cells per ml. RNAfrom these cells was extracted for RT-PCR to detect VEGF mRNA (see RNAExtraction and RT-PCR).

Fluorescence-Activated Cell Sorter Staining of VEGF-Expressing Cells

J774A.1 cells were treated with 0-8 μg/ml of ODN for 6-12 h. The cellswere then fixed in paraformaldehyde, blocked with FCS, and stained forVEGF by using biotinylated rat-anti-mVEGF164 antibody followed bystreptavidin-PE. Positive cells were identified by flow cytometry.

Statistical Analysis

Significant differences between groups were evaluated by using theStudent's t test. P 0.05 was regarded as significant difference betweentwo groups.

B. Neutralizing ODN Inhibits HSV DNA-Induced Angiogenesis

To investigate further whether CpG motifs in HSV DNA were responsiblefor the angiogenesis, HSV DNA was mixed with “neutralizing” or controlODN and the effect on angiogenesis recorded. The neutralizing ODNcontained multiple G-tetrad-forming motifs that other studies have shownto neutralize the immunostimulatory effects of CpG DNA (Krieg et al.,(1998) Proc. Natl. Acad. Sci. USA 95, 12631-12636; Lenert et al., (2001)Antisense Nucleic Acid Drug Dev. 11, 247-256; Pisetsky et al., (2000)Clin. Immunol. 96, 198-204). In these experiments, hydron pellets wereprepared that contained HSV DNA along with neutralizing or control ODN.Levels of angiogenesis were recorded at 4 days after implantation. As isevident, pellets that incorporated control ODN plus HSV DNA induced thesame level of angiogenesis as did HSV DNA pellets alone. In contrast,pellets containing neutralizing ODN plus HSV DNA induced significantlyless (60% inhibition) angiogenesis (P<0.01, FIG. 19).

While this disclosure has been described with an emphasis upon preferredembodiments, it will be obvious to those of ordinary skill in the artthat variations of the preferred embodiments may be used and it isintended that the disclosure may be practiced otherwise than asspecifically described herein. Accordingly, this disclosure includes allmodifications encompassed within the spirit and scope of the disclosureas defined by the following claims:

We claim:
 1. An oligodeoxynucleotide delivery complex comprising anoligodeoxynucleotide comprising the nucleic acid sequence set forth asSEQ ID NO: 3, wherein the oligodeoxynucleotide is modified to preventdegradation and wherein the oligodeoxynucleotide is at most 120nucleotides in length, has a CD value of at least 2.9 and suppresses animmune response; and a targeting moiety.
 2. The oligodeoxynucleotidedelivery complex of claim 1, wherein the targeting moiety is selectedfrom the group consisting of a cholesterol, a virosome, a liposome, alipid, and a target cell specific binding agent.
 3. Theoligodeoxynucleotide delivery complex of claim 2, wherein theoligodeoxynucleotide and the targeting moiety are covalently linked. 4.The oligodeoxynucleotide delivery complex of claim 1, wherein theoligodeoxynucleotide consists of the nucleic acid sequence set forth asSEQ ID NO:
 3. 5. The oligodeoxynucleotide delivery complex of claim 1,wherein the oligodeoxynucleotide has a CD value of greater than about3.2.
 6. The oligodeoxynucleotide delivery complex of claim 1, whereinthe oligodeoxynucleotide is at most 30 nucleotides in length.
 7. Animmunosuppressive composition comprising an effective amount of anoligodeoxynucleotide comprising the nucleic acid sequence set forth asSEQ ID NO: 3, wherein the oligodeoxynucleotide is modified to preventdegradation and wherein the oligodeoxynucleotide is at most 120nucleotides in length, has a CD value of at least 2.9 and suppresses animmune response; an additional agent; and a pharmacologically acceptablecarrier, wherein the additional agent is an anti-inflammatory agent, animmunosuppressive agent, or an anti-arthritis agent, and wherein thecomposition suppresses an immune response in a subject.
 8. Theimmunosuppressive composition of claim 7, wherein theoligodeoxynucleotide is 30 nucleotides in length.
 9. Theimmunosuppressive composition of claim 7, wherein the immunosuppressiveagent is a non-steroidal anti-inflammatory agent.
 10. Theimmunosuppressive composition of claim 7, wherein theoligodeoxynucleotide consists of the nucleic acid sequence set forth asSEQ ID NO:
 3. 11. The immunosuppressive composition of claim 7, whereinthe oligodeoxynucleotide comprises at most 20 guanosine-rich sequences.12. The immunosuppressive composition of claim 11, wherein theoligodeoxynucleotide comprises four guanosine-rich sequences.
 13. Amethod of suppressing an immune response in a subject comprisingadministering a therapeutically effective amount of theimmunosuppressive composition of claim 7 to a subject in which it isdesirable to suppress an immune response, thereby suppressing the immuneresponse in the subject.
 14. The method of claim 13, wherein theoligodeoxynucleotide is administered topically, parenterally, orally,intravenously, intra-muscularly, sub-cutaneously, inhalationally,nasally, topically, or intra-articularly.
 15. The method of claim 13,wherein the oligodeoxynucleotide is at most 30 nucleotides in length.16. The method of claim 13, further comprising administering anadditional anti-inflammatory or immunosuppressive agent to the subject.17. The composition of claim 7, wherein the anti-inflammatory agent isas diclofenac, diflunisal, etodolac, flurbiprofen, ibuprofen,indomethacin, ketoprofen, ketorolac, nabumetone, naproxen, oxaprozin,piroxicam, sulindac, tolmetin, celecoxib, and rofecoxib, steroids, suchas cortisone, dexamethasone, hydrocortisone, methylprednisolone,prednisolone, prednisone, and triamcinolone.
 18. A method of suppressingan immune response in a subject comprising administering atherapeutically effective amount of the oligonucleotide delivery complexof claim 1 to a subject in which it is desirable to suppress an immuneresponse, thereby suppressing the immune response in the subject.